pathotyprA fast, offline, pathogen-agnostic toolkit for lineage classification and marker-driven genotyping from whole-genome sequencing data. Bring your own SNP marker panel for any microbial pathogen — pathotypr handles the rest. Ships with curated panels for Mycobacterium tuberculosis complex (MTBC): 3,707 lineage-defining SNPs and over 102,000 resistance-associated mutations. Works with assembled genomes (FASTA) and raw reads (FASTQ). Available as command-line interface and cross-platform desktop GUI (Tauri).https://github.com/PathoGenOmics-Lab/pathotyprpathotyprbiotools:pathotypr1.0.0Command-line toolDesktop applicationhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_3301Microbiologyhttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_3305Public health and epidemiologyhttp://edamontology.org/topic_3474Machine learningRustAGPL-3.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_3196Genotypinghttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAtrain — Build a Random Forest classifier from labeled genomes.http://edamontology.org/operation_3225Variant classificationhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTApredict — Assign lineages to genomes using a pre-trained Random Forest model.http://edamontology.org/operation_3196Genotypinghttp://edamontology.org/operation_3225Variant classificationhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAclassify — Call known SNP markers in assembled genomes against a user-defined marker panel.http://edamontology.org/operation_3196Genotypinghttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1930FASTQsplit-fastq — Alignment-free genotyping directly from raw reads using k-mer matching.http://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1930FASTQmatch — Find the closest reference genome from a set of references for raw reads.https://github.com/PathoGenOmics-Lab/pathotypr/releasesBinarieshttps://github.com/PathoGenOmics-Lab/pathotyprSource codehttps://github.com/PathoGenOmics-Lab/pathotypr/tree/main/docsUser manual10.64898/2026.03.24.714002PrimaryPaula Ruiz-Rodriguezhttps://orcid.org/0000-0003-0727-5974PersonDeveloperMaintainerMireia Coscollahttps://orcid.org/0000-0003-0752-0538PersonPrimary contactI2SysBio (CSIC - Universitat de València)InstituteProviderPathoGenOmics LabDivisionProviderMHCclusterFunctional cluster of MHC class I molecules (MHCI) based on their predicted binding specificity.http://cbs.dtu.dk/services/MHCcluster/mhcclusterbiotools:mhccluster2.0Web applicationhttp://edamontology.org/topic_2830Immunoproteins, genes and antigensLinuxWindowsMacOtherEmergingFree of charge (with restrictions)http://edamontology.org/operation_3459Functional clusteringhttp://edamontology.org/data_1353Sequence motifhttp://edamontology.org/format_1929FASTAprovides heat-map and graphical tree-based visualizations of the functional relationship between MHC class I and class II variantshttp://cbs.dtu.dk/servicesSoftware cataloguehttp://www.cbs.dtu.dk/services/MHCcluster-2.0/instructions.phpGeneral10.1007/s00251-013-0714-923775223PMC3750724PrimaryCBSInstituteProviderMorten Nielsenmniel@cbs.dtu.dkhttp://orcid.org/0000-0001-7885-4311PersonPrimary contactHTSlibThe main purpose of HTSlib is to provide access to genomic information files, both alignment data (SAM, BAM, and CRAM formats) and variant data (VCF and BCF formats). The library also provides interfaces to access and index genome reference data in FASTA format and tab-delimited files with genomic coordinates. It is utilized and incorporated into both SAMtools and BCFtools.http://www.htslib.org/htslibbiotools:htslib1.01.11.21.2.11.31.3.11.3.21.41.4.11.51.61.71.81.91.101.10.11.10.21.111.121.131.141.151.15.11.161.171.181.191.201.21.11.221.22.11.22.21.231.23.1Libraryhttp://edamontology.org/topic_3071Data managementWindowsLinuxMacCMITAnimal and Crop GenomicsMatureFree of chargeOpen accesshttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/data_0924Sequence tracehttp://edamontology.org/format_3462CRAMhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_2573SAMhttp://edamontology.org/format_2572BAMhttp://edamontology.org/format_1930FASTQhttp://edamontology.org/data_3498Sequence variationshttp://edamontology.org/format_3020BCFhttp://edamontology.org/format_3016VCFhttps://github.com/samtools/htslibRepositoryhttp://www.htslib.org/support/#listsMailing listhttps://github.com/samtools/htslib/issuesIssue trackerhttp://www.htslib.org/download/Downloads pagehttp://www.htslib.org/doc/#manual-pagesUser manualsamtoolsusedBybcftoolsusedBy10.1093/gigascience/giab00733594436PMC7931820PrimaryHTSlib: C library for reading/writing high-throughput sequencing data.Wellcome Sanger Institutesamtools@sanger.ac.ukhttps://www.sanger.ac.uk/InstituteProviderPrimary contactSamtools Help mailing listhttps://lists.sourceforge.net/lists/listinfo/samtools-helpProjectSupportQUASTQUAST stands for QUality ASsessment Tool.
It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.http://quast.sourceforge.net/quastquastbiotools:quastv.5.3.0Workflowhttp://edamontology.org/topic_0196Sequence assemblyLinuxMacPerlPythonCGPL-2.0ONTeaterMatureFree of chargeOpen accesshttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_3180Sequence assembly validationhttp://edamontology.org/data_1234Sequence set (nucleic acid)http://edamontology.org/format_1929FASTA# Running quast on a eukaryotic genomequast -ek assembly.fa --out output_prefixhttps://github.com/ablab/quastRepositoryhttps://github.com/ablab/quast/issuesIssue trackerhttp://quast.bioinf.spbau.ru/General10.1093/bioinformatics/btt08623422339PMC3624806QUAST Supportquast.support@cab.spbu.ruPersonPrimary contactWEBnmaWEBnm@ provides quick, automated computation and analysis of low-frequency normal modes for protein structures.http://apps.cbu.uib.no/webnmawebnmabiotools:webnma3.5Web APISuitehttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0736Protein folds and structural domainsLinuxWindowsMacPythonGPL-3.0BiB toolsCBU toolsUiB toolsELIXIR-NOELIXIR-NorwayMatureFree of chargeOpen access3D-BioInfoNorwayhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_0244Protein flexibility and motion analysishttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBConstructs elastic network model from alpha carbon coordinates of the protein, and computes properties to describe large scale conformations. Computes normal modes, fluctuation profiles, inter-residue correlations, conformational overlap analysis and vector field representations. Structural amino acid profiles, and normal mode characteristics describing protein motion, visualized in plots and decorated structure visualizations. White space delimited tabular data for normal modes and the provided plotshttp://edamontology.org/operation_2487Protein structure comparisonhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/data_0886Structure alignmenthttp://edamontology.org/format_2200FASTA-like (text)http://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBPerforms comparative analysis of the normal modes of protein structures. Computes the Bhattacharyya Coefficient (BC) and the Root Mean Squared Inner Product (RMSIP) of aligned parts of the proteins. Alignment of sets of proteins to be compared. Multiple protein structures Heatmaps, dendrograms and structural amino acid profiles for visual comparison of structural similarity. White space delimited tabular data for the provided plotshttps://github.com/reuter-group/webnma3RepositoryIssue trackerhttps://elixir.no/helpdeskHelpdeskHelpdesk and support for ELIXIR Norway services.http://apps.cbu.uib.no/webnma3/howto/singleQuick start guidehttp://apps.cbu.uib.no/webnma3/qandaFAQhttp://apps.cbu.uib.no/webnma3/aboutGeneralCitation instructionsnumpyusesbiopythonusesmatplotlibusesmustangusesdsspuses10.1186/s12859-014-0427-625547242PMC4339738Primary2.010.1186/1471-2105-6-5215762993PMC1274249Primary1.0Nathalie ReuterNathalie.Reuter@uib.nohttp://www.cbu.uib.no/reuter/https://orcid.org/0000-0002-3649-7675PersonPrimary contactDeveloperSandhya P Tiwarihttps://orcid.org/0000-0002-0747-3826PersonDeveloperKidane M TeklePersonDeveloperTristan CragnoliniPersonDeveloperSvenn H GrindhaugPersonDeveloperLars SkjærvenPersonDeveloperGisle SalensmindePersonDeveloperEdvin FuglebakkPersonDeveloperSiv M HollupPersonDeveloperDepartment of Molecular Biology, University of Bergen, NorwayInstituteProviderComputational Biology Unit, Department of Informatics, University of Bergen, NorwayInstituteProviderUiBInstituteProviderMaplerMapler is a pipeline for assessing assembly quality in taxonomically rich metagenomes sequenced with HiFi reads. It incorporates state-of-the-art metrics and facilitates the comparison of assembly strategies.https://github.com/Nimauric/Maplermaplerbiotools:maplerWorkflowCommand-line toolhttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/topic_0196Sequence assemblyBashPythonAGPL-3.0Free of chargeOpen accesshttp://edamontology.org/operation_0310Sequence assemblyhttp://edamontology.org/data_0924Sequence tracehttp://edamontology.org/format_1930FASTQhttp://edamontology.org/operation_3180Sequence assembly validationhttp://edamontology.org/operation_3731Sample comparisonhttp://edamontology.org/data_1234Sequence set (nucleic acid)http://edamontology.org/format_1929FASTAhttp://edamontology.org/operation_3798Read binninghttp://edamontology.org/data_1234Sequence set (nucleic acid)http://edamontology.org/format_1929FASTAhttps://github.com/Nimauric/MaplerRepository10.1093/BIOINFORMATICS/BTAF33440478660PMC12205171Nicolas Mauricenicolas.maurice@inria.frhttps://orcid.org/0009-0009-9615-2765PersonClaire Lemaitrehttps://orcid.org/0000-0001-8675-170XRiccardo Vicedominihttps://orcid.org/0000-0002-7706-0998Clémence Friouxclemence.frioux@inria.frhttps://orcid.org/0000-0003-2114-0697PersonNetPhosNeural network predictions for serine, threonine and tyrosine phosphorylation sites in eukaryotic proteins.http://cbs.dtu.dk/services/NetPhos/netphosbiotools:netphos2.0Command-line toolWeb applicationWeb servicehttp://edamontology.org/topic_0160Sequence sites, features and motifsLinuxWindowsMacOtherEmergingFree of charge (with restrictions)http://edamontology.org/operation_3092Protein feature detectionhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAproduces neural network predictions for serine, threonine and tyrosine phosphorylation sites in eukaryotic proteinshttp://cbs.dtu.dk/servicesSoftware cataloguehttp://www.cbs.dtu.dk/services/NetPhos/instructions.phpGeneral10.1006/jmbi.1999.331010600390PrimaryCBSInstituteProviderhttp://www.bioinformatics.dtu.dk/english/Service/ContactPersonPrimary contactNicolaj Blomnblom@kt.dtu.dkhttp://orcid.org/0000-0001-7787-7853BigSeqKitThe Next Generation Sequencing (NGS) raw data are stored in FASTA and FASTQ text-based file formats. Common operations on FASTA/Q files include searching, filtering, sampling, deduplication and sorting, among others. We can find several tools in the literature for FASTA/Q file manipulation but none of them are well fitted for large files of tens of GB (likely TBs in the near future) since mostly they are based on sequential processing. The exception is seqkit that allows some routines to use a few threads but, in any case, the scalability is very limited. To deal with this issue, we introduce BigSeqKit, a parallel toolkit to manipulate FASTA/Q files at scale with speed and scalability at its core. BigSeqKit takes advantage of an HPC-Big Data framework (IgnisHPC) to parallelize and optimize the commands included in seqkit. In this way, in most cases it is from tens to hundreds of times faster than other state-of-the-art tools such as seqkit, samtools and pyfastx.https://github.com/citiususc/BigSeqKitbigseqkitbiotools:bigseqkitLibraryCommand-line toolhttp://edamontology.org/topic_0080Sequence analysisLinuxPythonGPL-3.0http://edamontology.org/operation_3192Sequence trimminghttp://edamontology.org/operation_0372DNA transcriptionhttp://edamontology.org/operation_0371DNA translationhttp://edamontology.org/operation_0233Sequence conversionhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_1929FASTAPLASTPLAST is a heuristical method to search for highest scoring local alignments between a DNA sequence query and a graphical pangenome. It takes as input a plain DNA sequence and a pangenome which may either be a set of (multiple) FASTA or FASTQ files or a sequence graph constructed by the tool Bifrost. It then outputs statistically meaningful (gapped) alignments in the style of the NCBI BLAST standard output format. Alignments are calculated based on a "seed-and-extend approach" while traversing the sequence graph. Biologically meaningful alignments are filtered by using an alignment statistic explicitly developed for sequence-to-graph alignments involving graphical pangenomes.https://github.com/tischulz1/plastpangenome-blastbiotools:pangenome-blast0.0.1-0.2.0Command-line toolhttp://edamontology.org/topic_0797Comparative genomicshttp://edamontology.org/topic_0080Sequence analysisLinuxMacWindowsC++GPL-3.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_0495Local alignmenthttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1211unambiguous pure nucleotidehttp://edamontology.org/data_1234Sequence set (nucleic acid)http://edamontology.org/format_3975GFA 1http://edamontology.org/format_2333Binary formatIn order to search for alignments within the pangenome graph,
A pangenome graph used to search for alignments consists of (1) a file in GFA format containing all sequences of the graph, (2) a binary file produced by the tool itself or the software "Bifrost" and (3) a program-specific index data structure in binary format.PLAST Search -i pangenomeGraphCommonFilePrefix -q fileContainingOneQueryPerLinehttp://edamontology.org/operation_0227Indexinghttp://edamontology.org/data_0850Sequence sethttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1930FASTQIf a pangenome graph already exists and only an index has to be built, FASTA/FASTQ files are not needed.PLAST Build -i pangenomeGraphCommonFilePrefix -R *.fastahttps://gitlab.ub.uni-bielefeld.de/gi/plastRepositoryhttps://github.com/tischulz1/plastMirrorhttps://gitlab.ub.uni-bielefeld.de/gi/plast/-/blob/master/README.mdGeneral10.1093/bioinformatics/btab07733532821PMC8388040PrimaryMethodBenchmarking studyBielefeld Universityhttps://www.uni-bielefeld.de/InstituteProviderGenome Informaticshttps://gi.cebitec.uni-bielefeld.de/InstituteProviderTizian Schulzplast-service@cebitec.uni-bielefeld.dehttps://orcid.org/0000-0003-0744-7078PersonDevelopercuffcompareCompare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments.http://cole-trapnell-lab.github.io/cufflinks/cuffcomparebiotools:cuffcompare2.2.1.0Web applicationhttp://edamontology.org/topic_3168SequencingLinuxWindowsMacC++CufflinksgalaxyPasteurMatureOpen accesshttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/data_0006Datahttp://edamontology.org/format_1975GFF3http://edamontology.org/format_2306GTFhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1929FASTAhttps://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/cuffcompare/cuffcompare/2.2.1.0Galaxy servicehttp://cole-trapnell-lab.github.io/cufflinks/cuffcompare/General10.1038/nbt.162120436464PMC3146043Primary10.1093/nar/gkw34327137889PMC4987906Other10.7490/f1000research.1114334.1OtherGalaxy Support Teamgalaxy@pasteur.frPersonPrimary contactfurThe program fur takes as input a set of target genome sequences and a set of related genome sequences, the neighbors. It returns the sequence regions common to all targets that are absent form the neighbors. Such regions can be used as candidate genetic markers.https://github.com/evolbioinf/furfurbiotools:furhttp://edamontology.org/topic_3344Biomedical scienceGohttp://edamontology.org/operation_2998Nucleic acid comparisonhttp://edamontology.org/data_2887Nucleic acid sequence recordhttp://edamontology.org/format_1929FASTAmetabuliMetabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acidhttps://metabuli.steineggerlab.commetabulibiotools:metabuliCommand-line toolDesktop applicationhttp://edamontology.org/topic_0637TaxonomyWindowsMacLinuxC++GPL-3.0MatureFree of chargehttp://edamontology.org/operation_3460Taxonomic classificationhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1929FASTAhttps://github.com/steineggerlab/Metabuli/issuesIssue trackerhttps://github.com/steineggerlab/MetabuliRepositorygithub repositorymmseqs2usesgtdbuses10.1038/s41592-024-02273-y38769467sourmashCompute and compare MinHash signatures for DNA data sets.https://sourmash.readthedocs.io/en/latest/sourmashbiotools:sourmash2.0a8LibraryCommand-line toolhttp://edamontology.org/topic_3697Microbial ecologyhttp://edamontology.org/topic_3174MetagenomicsLinuxMacBSD-3-ClauseEmergingFree of chargehttp://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/operation_0289Sequence distance matrix generationhttp://edamontology.org/data_2975Nucleic acid sequence (raw)http://edamontology.org/format_2200FASTA-like (text)http://edamontology.org/operation_3460Taxonomic classificationhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1930FASTQhttps://github.com/sourmash-bio/sourmashRepositorygithub repositorygtdbuses10.12688/f1000research.19675.131508216PMC6720031C. Titus Brownctbrown@ucdavis.eduhttp://github.com/dib-lab/sourmash/PersonPrimary contactBaktaRapid & standardized annotation of bacterial genomes, MAGs & plasmidshttps://github.com/oschwengers/baktabaktabiotools:baktav1.12.0Web applicationCommand-line toolhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0091BioinformaticsLinuxMacPythonGPL-3.0MatureFree of chargeOpen accessToolsGermanyhttp://edamontology.org/operation_0362Genome annotationhttp://edamontology.org/data_0925Sequence assemblyhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2914Sequence features metadatahttp://edamontology.org/format_3475TSVhttp://edamontology.org/data_2012Sequence coordinateshttp://edamontology.org/format_1975GFF3http://edamontology.org/data_2886Protein sequence recordhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1364Hidden Markov modelhttp://edamontology.org/format_3329HMMER3bakta --db <db-path> --prefix <prefix> --output <output-path> genome.fastahttps://github.com/oschwengers/baktaRepositoryhttps://github.com/oschwengers/bakta/issuesIssue trackerhttps://bioconda.github.io/recipes/bakta/README.htmlOtherhttps://bakta.computational.bioServicehttps://zenodo.org/records/14916843OtherMandatory annotation databasev6.0https://github.com/oschwengers/bakta/blob/main/README.mdGeneralhttps://github.com/oschwengers/bakta/blob/main/CONTRIBUTION.mdContributions policyhttps://github.com/oschwengers/bakta/blob/main/CODE_OF_CONDUCT.mdCode of conducthttps://bakta.readthedocs.io/User manualdiamonduseshmmer3usesinfernalusestrnascan-seusesblastusesaragornusespilercrusesdeepsiguses10.1099/mgen.0.00068534739369PMC8743544Primary1.110.1093/nar/gkaf33540271661PMC12230652PrimaryOliver Schwengersoliver.schwengers@cb.jlug.dehttps://github.com/oschwengershttps://orcid.org/0000-0003-4216-2721PersonPrimary contactDeveloperMaintainerJustus Liebig University Giessenhttps://www.uni-giessen.deInstituteProviderMetaPhlAnComputational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.http://segatalab.cibio.unitn.it/tools/metaphlan/index.htmlmetaphlanbiotools:metaphlanCommand-line toolhttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/topic_0194PhylogenomicsLinuxMacWindowsPythonMITAnimal and Crop Genomicshttp://edamontology.org/operation_3460Taxonomic classificationhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_2573SAMhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1930FASTQmetaphlan <fastq_input> --input_type fastq -o <output>http://edamontology.org/operation_3460Taxonomic classificationhttp://edamontology.org/data_3028Taxonomyhttp://edamontology.org/format_3751DSVConvert SGB-based profile to GTDB taxonomysgb_to_gtdb_profile.py -i <metaphlan_output> -o <gtdb_metaphlan_output>https://github.com/biobakery/MetaPhlAnGeneralgtdbuses10.1038/nmeth.206622688413PMC3443552Primaryhttps://groups.google.com/forum/#!forum/metaphlan-usersPersonPrimary contactkraken2Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.
Any assumption that Kraken’s raw read assignments can be directly translated into species or strain-level abundance estimates is flawed. Bracken (Bayesian Reestimation of Abundance after Classification with KrakEN), estimates species abundances in metagenomics samples by probabilistically re-distributing reads in the taxonomic tree. (Lu, Jennifer et al. “Bracken: estimating species abundance in metagenomics data.”)https://github.com/DerrickWood/kraken2kraken2biotools:kraken22.0.8-betaCommand-line toolhttp://edamontology.org/topic_0637Taxonomyhttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/topic_3697Microbial ecologyhttp://edamontology.org/topic_3301MicrobiologyPerlC++MITONTeaterFree of chargeOpen accesshttp://edamontology.org/operation_3460Taxonomic classificationhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_1929FASTA`kraken2 --db <kraken2_database> <input.fastq>`https://github.com/DerrickWood/kraken2Repositoryhttps://github.com/DerrickWood/kraken2/issuesIssue trackerhttps://github.com/DerrickWood/kraken2/archive/v2.0.8-beta.tar.gzSource code2.0.8-betahttps://github.com/DerrickWood/kraken2/wiki/ManualUser manualhttps://benlangmead.github.io/aws-indexes/k2User manualLinks to multiple Kraken 2 and bracken databases and indexeskrakenisNewVersionOfbrackenusedBygtdbuses10.1101/762302Derrick E. Woodhttp://orcid.org/0000-0002-7429-1854PersonJennifer Luhttp://orcid.org/0000-0001-9167-2002PersonBen Langmeadlangmea@cs.jhu.eduhttp://orcid.org/0000-0003-2437-1976PersonSingleMNovelty-inclusive microbial community profiling of shotgun metagenomeshttps://wwood.github.io/singlem/singlembiotools:singlemCommand-line toolhttp://edamontology.org/topic_3174MetagenomicsLinuxPythonGPL-3.0Free of chargeOpen accesshttp://edamontology.org/operation_3460Taxonomic classificationhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_1929FASTAhttps://wwood.github.io/singlem/GeneralCommand-line optionsInstallation instructionsgtdbusesglobdbuses10.1101/2024.01.30.578060FastOMAFastOMA is a scalable software package to infer orthology relationship.https://github.com/dessimozlab/FastOMAfastomabiotools:fastoma0.5.1Command-line toolhttp://edamontology.org/topic_0797Comparative genomicsMacLinuxPythonMPL-2.0MatureFree of chargeOpen accessSwitzerlandhttp://edamontology.org/operation_3947Phylogenetic tree reconciliationhttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_3209Genome comparisonhttp://edamontology.org/operation_0291Sequence clusteringhttp://edamontology.org/operation_0540Phylogenetic inference (from molecular sequences)http://edamontology.org/data_2886Protein sequence recordhttp://edamontology.org/format_2200FASTA-like (text)http://edamontology.org/data_3028Taxonomyhttp://edamontology.org/format_1910newickhttps://github.com/dessimozlab/FastOMARepositoryhttps://omabrowser.orgServicehttps://github.com/DessimozLab/FastOMA/blob/main/README.mdQuick start guideomameruses10.1038/s41592-024-02552-839753922PMC11810774globalamfungiThe GlobalAMFungi Database is an open-access, global repository of arbuscular mycorrhizal (AM) fungal occurrence data compiled from high-throughput sequencing studies. It aggregates millions of DNA sequence observations of AM fungi from thousands of geographically referenced environmental samples, together with rich metadata on sampling location and environmental context, to map the global distribution and diversity of these key plant symbionts. The resource is designed to be community-driven and FAIR (Findable, Accessible, Interoperable, Reusable), supporting research into AM fungal ecology, biogeography, and how environmental factors shape their diversity.https://globalamfungi.com/globalamfungibiotools:globalamfungiDatabase portalWeb applicationhttp://edamontology.org/topic_3050Biodiversityhttp://edamontology.org/topic_3697Microbial ecologyhttp://edamontology.org/topic_3810Agricultural scienceRCC-BY-4.0ELIXIR-CZCzech RepublicMatureFree of chargeOpen accessDataPlant SciencesCzech Republichttp://edamontology.org/operation_3431Data depositionhttp://edamontology.org/operation_0226Annotationhttp://edamontology.org/operation_3460Taxonomic classificationhttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1929FASTAhttps://globalamfungi.com/HelpdeskRepositoryServicehttps://globalamfungi.com/User manualCitation instructionsQuick start guideContributions policyGeneral10.1111/nph.19283PrimaryTomas Vetrovskyvetrovsky@biomed.cas.czhttps://orcid.org/0000-0002-0831-486X02p1jz666PersonPrimary contactDeveloperContributorELIXIR-CZConsortiumASAFindASAFind is a software that predicts the intracellular location of proteins in cells with four membrane-bound complex plastids of red algal origin.
These plastids evolved via eukaryote-eukaryote endosymbiosis and for example can be found in diatoms and cryptophytes. ASAFind uses protein sequence data and external predictions of signal peptides (by the tools SignalP and TargetP), and predicts plastid proteins, and proteins that are targeted to the periplastidic compartment from these data; optionally, a graphical output can generated.https://asafind.jcu.cz/asafindbiotools:asafind2.0ScriptCommand-line toolWeb servicehttp://edamontology.org/topic_2229Cell biologyhttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_0780Plant biologyhttp://edamontology.org/topic_0622GenomicsMacLinuxPythonCC-BY-SA-4.0ELIXIR-CZCzech RepublicMatureFree of chargeOpen accessToolsPlant SciencesMarine MetagenomicsMicrobial BiotechnologyCzech Republichttp://edamontology.org/operation_2489Subcellular localisation predictionhttp://edamontology.org/operation_0239Sequence motif recognitionhttp://edamontology.org/operation_0422Protein cleavage site predictionhttp://edamontology.org/data_2886Protein sequence recordhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1270Feature tablehttps://asafind.jcu.czServiceWeb Servicehttps://github.com/ASAFind/ASAFind-2RepositoryInformation and source code, for local installation or developmenthttps://asafind.jcu.cz/download-page/Downloads pageDownload page on web-service, links to repository2.0https://asafind.jcu.cz/download-page/Installation instructionssignalpusestargetpuses10.1111/tpj.7013840464854PMC12136025Primary2.0Publication of the current version of ASAFind (2.0)10.1111/tpj.1273425438865PMC4329603Other1.0Publication of the first version of ASAFind10.48550/arXiv.2303.02509Benchmarking study1.0Benchmarking of the performance of the first version of ASAFindMarta Vohnoutovámvohnoutova@jcu.czhttps://www.jcu.cz/cz/univerzita/lide/clovek?identita=Vohnoutova_Marta_61699https://orcid.org/0000-0002-8915-8626PersonContributorDeveloperMaintainerAnsgar Gruberagruber@prf.jcu.czhttps://www.jcu.cz/cz/univerzita/lide/clovek?identita=Gruber_Ansgar_118401https://orcid.org/0000-0002-5876-4391PersonPrimary contactDeveloperDocumentormetagWGSmetagWGS is a workflow dedicated to the analysis of metagenomic data. It allows assembly, taxonomic annotation, and functional annotation of predicted genes. Since release 2.3, binning step with the possibility of cross-alignment is included. It has been developed in collaboration with several CATI BIOS4biol agents. Funded by Antiselfish Project (Labex Ecofect), ExpoMicoPig project (France Futur elevage) and SeqOccIn project (CPER - Occitanie Toulouse / FEDER), ATB_Biofilm funded by PNREST Anses, France genomique (ANR-10-INBS-09-08) and Resalab Ouest.https://forgemia.inra.fr/genotoul-bioinfo/metagwgsmetagwgsbiotools:metagwgs2.32.5.0Workflowhttp://edamontology.org/topic_3174MetagenomicsLinuxPythonGPL-3.0MatureFree of chargeOpen accessFrancehttp://edamontology.org/operation_3460Taxonomic classificationhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1930FASTQhttp://edamontology.org/operation_3672Gene functional annotationhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/operation_0524De-novo assemblyhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1930FASTQhttps://forge.inrae.fr/genotoul-bioinfo/metagwgsRepositorySee documentation, source code and functionnal test documentation.https://forgemia.inra.fr/genotoul-bioinfo/metagwgs-test-datasetsTest dataFunctional tests data and scripthttps://genotoul-bioinfo.pages-forge.inrae.fr/metagwgs/master/index.htmlUser manualWe provide up to date installation documentation, usage documentation, output description and functionnal test datasets and procedure.Claire Hoedeclaire.hoede@inrae.frhttps://orcid.org/0000-0001-5054-7731PersonPrimary contactGenoToul bioinformatics facilityhttp://bioinfo.genotoul.fr/DivisionProviderJalviewJalview is a free cross-platform program for multiple sequence alignment editing, visualisation and analysis. Use it to align, view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation.https://www.jalview.org/Jalviewbiotools:Jalview2.11.5.1Desktop applicationCommand-line toolhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0092Data visualisationMacLinuxWindowsGPL-3.0ELIXIR-UKMatureFree of chargeOpen accessToolsInteroperabilityUKhttp://edamontology.org/operation_3081Sequence alignment editinghttp://edamontology.org/operation_0324Phylogenetic tree analysishttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1948nbrf/pirhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1984FASTA-alnhttp://edamontology.org/format_3015Pileuphttp://edamontology.org/format_1938GFF2-seqhttp://edamontology.org/format_3313BLChttp://edamontology.org/format_3311RNAMLhttp://edamontology.org/format_1915Formathttp://edamontology.org/format_3774BioJSON (Jalview)http://edamontology.org/format_1982ClustalW formathttp://edamontology.org/format_1477mmCIFhttp://edamontology.org/format_1997PHYLIP formathttp://edamontology.org/format_3016VCFhttp://edamontology.org/format_1961Stockholm formathttp://edamontology.org/format_1939GFF3-seqhttp://edamontology.org/format_1947GCG MSFhttp://edamontology.org/data_0886Structure alignmenthttp://edamontology.org/format_1476PDBOther Input formats:
AMSA (.amsa);
JnetFile (.concise, .jnet);
PFAM (.pfam);
Substitution matrix (.matrix);
Jalview Project File (.jvp);
Jalview Feature File (.features, .jvfeatures);
Jalview Annotations File (.annotations, .jvannotations);
Predicted Aligned Error (PAE) Matrix File (.json)
...
Other Output formats:
PFAM (.pfam);
BioJS (.biojs) (interactive HTML/Javascript);
Jalview Project File (.jvp);https://discourse.jalview.org/Discussion forumhttps://issues.jalview.org/Issue trackerhttps://www.jalview.org/development/jalview_develop/OtherLatest development versionhttps://gitlab.jalview.org/jalview/jalview.gitRepositoryhttps://twitter.com/JalviewSocial mediaTwitter feedhttps://www.youtube.com/channel/UCIjpnvZB770yz7ftbrJ0tfwSocial mediaYouTube training videoshttps://www.linkedin.com/company/104771886/Social mediahttps://www.jalview.org/downloadDownloads pagehttps://www.jalview.org/download/source/Source codehttps://www.jalview.org/download/?os=allBinariesBinaries for all platformshttps://www.jalview.org/favicon.svgIconhttps://www.jalview.org/download/other/jar/BinariesExecutable JAR filehttps://www.jalview.org/about/citationCitation instructionshttps://www.jalview.org/training/Training materialHands-on exercises, Training courses and Training videoshttps://www.jalview.org/help/faqFAQhttps://www.jalview.org/help/documentation/User manualjabawsuseschimerauseschimeraxusespymolusesbiocondaincludedIn3d-beaconsusesuniprotusespfamusesensemblusespdbusesrfamuses3d-beaconsuses10.1093/bioinformatics/btp03319151095PMC2672624Jim Procterhttp://www.lifesci.dundee.ac.uk/people/jim-procterhttps://orcid.org/0000-0002-7865-7382PersonPrimary contactGeoff Bartonhttps://www.lifesci.dundee.ac.uk/people/geoff-bartonhttps://orcid.org/0000-0002-9014-5355emapper2gbkcreation of genbank files from Eggnog-mapper annotation outputshttps://github.com/AuReMe/emapper2gbkemapper2gbkbiotools:emapper2gbk0.3.2Command-line toolhttp://edamontology.org/topic_4011Data rescueLinuxPythonLGPL-3.0AuReMeMatureFree of chargeOpen accesshttp://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_0925Sequence assemblyhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1233Sequence set (protein)http://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2012Sequence coordinateshttp://edamontology.org/format_2305GFFGenomic -single modegenomes -fn genome.fna -fp proteome.faa -gff genome.gff -n "Escherichia coli"https://github.com/AuReMe/emapper2gbkRepositoryhttps://pypi.org/project/emapper2gbk/Software catalogueAccess to Python libraryhttps://github.com/AuReMe/emapper2gbk.gitSource code0.3.2https://pypi.org/project/emapper2gbk/#filesSoftware package0.3.2https://github.com/AuReMe/emapper2gbkInstallation instructionsUser manualArnaudhttps://github.com/ArnaudBelcourhttps://orcid.org/0000-0003-1170-0785PersonDeveloperSouth Green Genome HubsThe South Green Genome Hub is a suite of crop-specific community portals to manage genomic datasets with focus on tropical and Mediterranean plants. Currently developed on Banana, Cacao, Coffee, Grass, Rice, Vanilla, Citrus and Sugarcane, genome hubs provide access to multiple datasets (e.g. assemblies, gene product information, metabolic pathways, gene families, transcriptomics and genetic markers).https://banana-genome-hub.southgreen.fr/South_Green_Genome_Hubsbiotools:South_Green_Genome_HubsDatabase portalhttp://edamontology.org/topic_3810Agricultural sciencehttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_0797Comparative genomicshttp://edamontology.org/topic_0621Model organismsJavaScriptPHPGPL-2.0Genome HubMatureFree of chargeDataToolsFrancehttp://edamontology.org/operation_3208Genome visualisationhttp://edamontology.org/operation_0338Sequence database searchhttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/data_0968Keywordhttp://edamontology.org/format_1929FASTAhttps://github.com/SouthGreenPlatform/genomehubsIssue trackerhttps://banana-genome-hub.southgreen.fr/content/term-serviceTerms of usetripalusesbanana_genome_hubincludescoffee_genome_hubincludescocoa_genome_hubincludesrice_genome_hubincludessugarcane_genome_hubincludessouthgreenincludedIn10.1093/database/bat03523707967PMC3662865Primary10.1093/nar/gku110825392413PMC4383925Primary10.1093/hr/uhac22136479579PMC9720444Primary10.1016/j.xplc.2022.10033035617961PMC9482989UsageGaetan Drocdroc@cirad.frhttps://orcid.org/0000-0003-1849-1269PersonPrimary contactDeveloperDocumentorProviderSupportAlexis Dereeperalexis.dereeper@ird.frMathieu Rouardm.rouard@cgiar.orghttps://orcid.org/0000-0003-1849-1269Primary contactMaintainerSupportValentin Guignonv.guignon@cgiar.orgChrisitine Tranchantchristine.tranchant@ird.frStéphanie Bocsstephanie.sidibe-bocs@cirad.frtrimAlTool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment.https://trimal.readthedocs.iotrimalbiotools:trimal1.5.12.0-RCCommand-line toolhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0160Sequence sites, features and motifsMacWindowsLinuxC++MatureFree of chargehttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/data_0863Sequence alignmenthttps://github.com/inab/trimalRepositoryhttps://github.com/inab/trimalSource code1.5.1https://github.com/inab/trimal/tree/2.0_RCSource code2.0-RChttp://trimal.cgenomics.org/GeneralOld versionshttps://trimal.readthedocs.ioGeneral10.1093/bioinformatics/btp34819505945PMC2712344Salvador Capella-Gutierrezsalcagu@gmail.comPersonPrimary contacttgabaldon@crg.eshttp://gabaldonlab.crg.es/PersonPrimary contactMMseqs2MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed.
MMseqs2 includes Linclust, the first clustering algorithm whose runtime scales linearly With Linclust we clustered 1.6 billion metagenomic sequence fragments in 10 h on a single server to 50% sequence identity.https://mmseqs.comMMseqs2biotools:MMseqs2Command-line toolhttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_0077Nucleic acidshttp://edamontology.org/topic_0623Gene and protein familieshttp://edamontology.org/topic_0637TaxonomyWindowsLinuxMacC++MITMatureFree of chargeOpen accesshttp://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_0850Sequence sethttp://edamontology.org/format_2182FASTQ-like format (text)http://edamontology.org/format_2200FASTA-like (text)mmseqs easy-search query.fasta target.fasta output.m8 tmphttp://edamontology.org/operation_0291Sequence clusteringhttp://edamontology.org/data_0850Sequence sethttp://edamontology.org/format_2182FASTQ-like format (text)http://edamontology.org/format_2200FASTA-like (text)mmseqs easy-cluster input.fasta output tmp
mmseqs easy-linclust input.fasta output tmphttp://edamontology.org/operation_3460Taxonomic classificationhttp://edamontology.org/data_0850Sequence sethttp://edamontology.org/format_2182FASTQ-like format (text)http://edamontology.org/format_2200FASTA-like (text)mmseqs easy-taxonomy query.fasta targetDB output tmphttps://github.com/soedinglab/mmseqs2/issuesIssue trackerhttps://github.com/soedinglab/mmseqs2Repositoryhttps://github.com/soedinglab/MMseqs2/releasesSource codehttps://github.com/soedinglab/MMseqs2/blob/master/README.mdGeneralhttps://github.com/soedinglab/mmseqs2/wikiUser manualhttps://github.com/soedinglab/MMseqs2/wiki/TutorialsTraining materialTutorial materialmmseqsisNewVersionOfplassusedBylinclustincludesmetaeukusedByconterminatorusedByspacepharerusedBy10.1038/nbt.39882903537210.1101/07968110.1038/s41467-018-04964-529959318PMC6026198Method10.1093/bioinformatics/bty105730615063PMC6691333Method10.1101/2020.11.27.40101810.1093/bioinformatics/btab18433734313PMC8479651MMseqs2 Taxonomy10.1101/2024.11.13.623350v1MMseqs2-GPU preprint10.1038/s41592-025-02819-8MMseqs2-GPUprolfquappA command-line tool for differential expression analysis in quantitative proteomicshttps://github.com/prolfqua/prolfquappprolfquappbiotools:prolfquapp0.1.6Command-line toolhttp://edamontology.org/topic_0121ProteomicsMacLinuxRMITEmergingFree of chargeOpen accesshttp://edamontology.org/operation_3741Differential protein expression profilinghttp://edamontology.org/data_2603Expression datahttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_3475TSVhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTA./prolfqua_dea.sh -i data_dir/ -d annotation.xlsx -y config.yaml -w NameOfAnalysis -s DIANN
# and again you run the version within the docker container with
# ./prolfquapp_docker.sh prolfqua_dea.sh -i data_dir/ -d annotation.xlsx -y config.yaml -w NameOfAnalysis -s DIANNhttp://edamontology.org/operation_2428Validationhttp://edamontology.org/data_2603Expression datahttp://edamontology.org/format_3620xlsxhttp://edamontology.org/operation_0571Expression data visualisationhttp://edamontology.org/data_2603Expression datahttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_3475TSVhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTAhttps://github.com/prolfqua/prolfquappRepositoryhttps://github.com/prolfqua/prolfquapp/issuesIssue trackerhttps://github.com/prolfqua/prolfquapp/releases/tag/0.1.6Downloads page0.1.6https://github.com/prolfqua/prolfquapp/blob/master/README.mdGeneral10.1021/acs.jproteome.4c00911Primary0.0.6PeptideShakerPeptideShaker is a search engine independent platform for interpretation of proteomics identification results from multiple search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot, Andromeda and mzIdentML. By combining the results from multiple search engines, while re-calculating PTM localization scores and redoing the protein inference, PeptideShaker attempts to give you the best possible understanding of your proteomics datahttp://compomics.github.io/projects/peptide-shaker.htmlpeptideshakerbiotools:peptideshaker3.0.11Desktop applicationCommand-line toolhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_0644ProteomeMacLinuxJavaApache-2.0de.NBIProteomicsBioInfra.ProtOpen accesshttp://edamontology.org/operation_3694Mass spectrum visualisationhttp://edamontology.org/operation_3631Peptide identificationhttp://edamontology.org/operation_2428Validationhttp://edamontology.org/operation_3755PTM localisationhttp://edamontology.org/operation_3501Enrichment analysishttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_3767Protein identificationhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0945Peptide identificationhttp://edamontology.org/format_3247mzIdentMLhttp://edamontology.org/data_2536Mass spectrometry datahttp://edamontology.org/format_3651MGFhttps://github.com/compomics/peptide-shakerSource codehttp://compomics.github.io/projects/peptide-shaker.html#read-meGeneral10.1038/nbt.310925574629PrimaryBioInfra.ProtInstituteProviderDominik Kopczynskdominik.kopczynski@isas.dehttp://compomics.github.io/projects/peptide-shaker.htmlPersonPrimary contactNGPSimulation of next-generation proteomics (NGP) based on single-molecule sequencing.https://github.com/magnuspalmblad/NGPngpbiotools:ngphttp://edamontology.org/operation_2426Modelling and simulationhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTA10.1021/acs.jproteome.1c0013633904308PMC8185883PrimaryNetStartPrediction of eukaryotic translation initiation sites using a protein language model.
NetStart 2.0 is a deep learning-based model that predicts canonical translation initiation sites in mRNA transcripts in species across the eukaryotic domain, including vertebrates, invertebrates, plants, fungi, and protists.
The model integrates the ESM-2 protein language model for assessing transitions from non-coding to coding regions with local start codon sequence context and taxonomical information. It has been trained on sequences from 60 phylogenetically diverse eukaryotic species.
If you need help with the bioinformatics programs, see the "Getting Help" section at the server site at the link.https://services.healthtech.dtu.dk/services/NetStart-2.0/netstart_2.0biotools:netstart_2.02.0http://edamontology.org/topic_3512Gene transcriptshttp://edamontology.org/topic_0108Protein expressionhttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_0621Model organismsMacLinuxPythonhttp://edamontology.org/operation_3767Protein identificationhttp://edamontology.org/operation_0362Genome annotationhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/operation_0439Translation initiation site predictionhttp://edamontology.org/data_3495RNA sequencehttp://edamontology.org/format_1929FASTAhttps://github.com/lsandvad/netstart2RepositoryGitHub with code and instructions and to download and run the program locallyhttps://services.healthtech.dtu.dk/services/NetStart-2.0/ServiceNetStart 2.0 server where sequences can be uploaded directly without having to download the program (hosted by DTU Health Tech).10.1186/S12859-025-06220-240830753PMC12366053Method2.0Line Sandvad Nielsenline.s.nielsen@bio.ku.dkPersonHenrik Nielsenhenni@dtu.dkPersonMS AnnikaMS Annika is a crosslink search engine based on MS Amanda, aimed at identifying crosslinks of cleavable and non-cleavable crosslinkers from MS2 and MS3 spectra. It can deal with a wide variety of cross-linkers and provides robust and transparent FDR control based on a target-decoy approach. MS Annika is available free of charge as a plug-in for Proteome Discoverer.https://github.com/hgb-bin-proteomics/MSAnnikams_annikabiotools:ms_annikaProteome Discoverer 3.2: MS Annika 3.0 v3.0.7Proteome Discoverer 3.1: MS Annika 3.0 v3.0.7Proteome Discoverer 3.0: MS Annika 2.0 v1.1.4fixProteome Discoverer 2.5: MS Annika 2.0 v1.1.3Proteome Discoverer 2.4: MS Annika v1.0.0Proteome Discoverer 2.3: MS Annika v1.0.0Plug-inhttp://edamontology.org/topic_0130Protein folding, stability and designhttp://edamontology.org/topic_0736Protein folds and structural domainshttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0091BioinformaticsWindowsC#FreewareMatureFree of chargeOpen accesshttp://edamontology.org/operation_3631Peptide identificationhttp://edamontology.org/operation_3646Peptide database searchhttp://edamontology.org/operation_3755PTM localisationhttp://edamontology.org/operation_3645PTM identificationhttp://edamontology.org/operation_3649Target-Decoyhttp://edamontology.org/data_0943Mass spectrumhttp://edamontology.org/format_3651MGFhttp://edamontology.org/format_3712Thermo RAWhttp://edamontology.org/data_2886Protein sequence recordhttp://edamontology.org/format_1929FASTAhttps://github.com/hgb-bin-proteomics/MSAnnikaRepositoryMS Annika version archivehttps://github.com/hgb-bin-proteomics/MSAnnika/raw/master/releases/latest/PD3.2/latest.zipSoftware packageLatest MS Annika version for Proteome Disoverer 3.2PD3.2:latesthttps://github.com/hgb-bin-proteomics/MSAnnika/raw/master/releases/latest/PD3.1/latest.zipSoftware packageLatest MS Annika version for Proteome Disoverer 3.1PD3.1:latesthttps://github.com/hgb-bin-proteomics/MSAnnika/raw/master/releases/latest/PD3.0/latest.zipSoftware packageLatest MS Annika version for Proteome Disoverer 3.0PD3.0:latesthttps://github.com/hgb-bin-proteomics/MSAnnika/raw/master/releases/latest/PD2.5/latest.zipSoftware packageLatest MS Annika version for Proteome Disoverer 2.5PD2.5:latesthttps://hgb-bin-proteomics.github.io/MSAnnika/Generalhttps://github.com/hgb-bin-proteomics/MSAnnika/raw/master/MS_Annika_3.0_UserManual.pdfUser manualhttps://github.com/hgb-bin-proteomics/MSAnnika/raw/master/tutorial/MS_Annika_3.0_Tutorial.pdfTraining materialDetailed tutorial how to use MS Annikahttps://www.youtube.com/watch?v=L1lVt35PYv4Training materialDetailed tutorial how to use MS Annikams_amandauses10.1021/acs.jproteome.0c0100033852321PMC8155564Primary1.0MS Annika for cleavable crosslink identification from MS2 spectra10.1021/acs.jproteome.3c0032537566781PMC10476269Primary2.0MS Annika 2.0 for cleavable crosslink identification from MS3 spectra10.1038/s42004-024-01386-x39702463PMC11659399Primary3.0MS Annika 3.0 for non-cleavable crosslink identificationViktoria Dorferviktoria.dorfer@fh-hagenberg.athttp://bioinformatics.fh-hagenberg.at/https://orcid.org/0000-0002-5332-5701PersonPrimary contactMicha Birklbauermicha.birklbauer@fh-hagenberg.athttp://bioinformatics.fh-hagenberg.at/https://orcid.org/0009-0005-1051-179XPersonDeveloperEPIKPrecise and scalable evolutionary placement with informative k-mers.https://github.com/phylo42/EPIKepikbiotools:epik0.2.0Command-line toolhttp://edamontology.org/topic_0084PhylogenyLinuxMacC++PythonMITEmergingFree of chargeOpen accesshttp://edamontology.org/operation_0323Phylogenetic inferencehttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0955Data indexhttp://edamontology.org/format_2333Binary format10.1093/BIOINFORMATICS/BTAD69237975872PMC107010970.2.0Nikolai Romashchenkonromashchenko@lirmm.frhttps://orcid.org/0000-0002-2264-5219PersonEric Rivalsrivals@lirmm.frhttps://orcid.org/0000-0003-3791-3973PersonSQUARNASQUARNA is a tool for RNA secondary structure prediction. It can take a single RNA sequence or an alignment of sequences as input. SQUARNA handles pseudoknots and can predict alternative structures. SQUARNA allows structural restraints and chemical probing data as additional input and is available at https://github.com/febos/SQUARNA.https://github.com/febos/SQUARNAsquarnabiotools:squarna2.3Command-line toolScriptLibraryhttp://edamontology.org/topic_3307Computational biologyhttp://edamontology.org/topic_0077Nucleic acidshttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_0097Nucleic acid structure analysishttp://edamontology.org/topic_0082Structure predictionhttp://edamontology.org/topic_0099RNAhttp://edamontology.org/topic_0659Functional, regulatory and non-coding RNAhttp://edamontology.org/topic_3511Nucleic acid sites, features and motifsMacLinuxWindowsPythonApache-2.03D-BioInfo-Nucleic-AcidEmergingFree of chargeOpen accesshttp://edamontology.org/operation_0278RNA secondary structure predictionhttp://edamontology.org/data_3495RNA sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1961Stockholm formathttp://edamontology.org/format_1982ClustalW formathttp://edamontology.org/data_1383Nucleic acid sequence alignmenthttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1961Stockholm formathttp://edamontology.org/format_1982ClustalW formathttp://edamontology.org/data_0889Structural profileInput can be a single or several RNA sequences or an alignment of RNA sequences along with structural restraints and/or chemical probing data on base reactivitiesSQUARNA i=inputfile [OPTIONS]https://github.com/febos/SQUARNARepositoryGitHub repositoryhttps://pypi.org/project/SQUARNA/Software cataloguePyPi repository pagehttps://doi.org/10.5281/zenodo.8292325Downloads page2.3https://pypi.org/project/SQUARNA/Software packagepip install SQUARNA2.3https://github.com/febos/SQUARNA/blob/main/README.mdUser manualhttps://pypi.org/project/SQUARNA/Installation instructionspip install SQUARNA10.1101/2023.08.28.555103biorxiv preprintEugene F Baulinefbaulin@gmail.comhttps://scholar.google.com/citations?user=sjfDaUwAAAAJ&hl=enhttps://orcid.org/0000-0003-4694-9783PersonDeveloperPrimary contactSupporthttps://imol.institute/leaders/baulin-group/REPETThe REPET package integrates bioinformatics pipelines dedicated to detect, annotate and analyze transposable elements (TEs) in genomic sequences. The main pipelines are (i) TEdenovo, which search for interspersed repeats, build consensus sequences and classify them according to TE features, and (ii)
TEannot, which mines a genome with a library of TE sequences, for instance the one produced by the TEdenovo pipeline, to provide TE annotations exported into GFF3 files.https://urgi.versailles.inrae.fr/Tools/REPETrepetbiotools:repetv3.0Command-line toolhttp://edamontology.org/topic_0157Sequence composition, complexity and repeatshttp://edamontology.org/topic_0654DNAhttp://edamontology.org/topic_0097Nucleic acid structure analysisLinuxMacC++PythonCECILL-2.0REPETelixir-fr-sdp-2019URGILegacyFree of chargeOpen accessToolsFrancehttp://edamontology.org/operation_0379Repeat sequence detectionhttp://edamontology.org/operation_0237Repeat sequence analysishttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1929FASTAhttps://urgi.versailles.inrae.fr/download/repet/Repositoryhttps://urgi.versailles.inrae.fr/download/repet/REPET_linux-x64-3.0.tar.gzSource codev3.0https://urgi.versailles.inrae.fr/Tools/REPETGeneralsee also https://urgi.versailles.inrae.fr/Tools/REPET/READMEhttps://urgi.versailles.inrae.fr/Tools/REPET/INSTALLInstallation instructionshttps://urgi.versailles.inrae.fr/Tools/REPET/TEdenovo-tutoUser manualSee also https://urgi.versailles.inra.fr/Tools/REPET/TEannot-tutohttps://forgemia.inra.fr/urgi-anagen/wiki-repet/-/wikis/REPET-V3.0-tutorialTraining material10.1371/journal.pone.009192924786468PMC4008368Primary10.1371/journal.pone.001652621304975PMC3031573Primary10.1371/journal.pcbi.001002216110336PMC1185648Primary10.1007/s00239-003-0007-215008403Method10.1109/JPROC.2016.2590833MethodURGIurgi-repet@versailles.inrae.frhttp://urgi.versailles.inrae.fr/InstituteDeveloperContributorMaintainerProviderSupportDocumentorThis tool has a "Numero de depot APP": FR 001 480007 000 R P 2008 000 31 235fqcleanerMini workflow for preprocessing fastq files, it includes quality trimming, duplicate and artefacts filters for FASTQ read files.https://gensoft.pasteur.fr/docs/fqCleanER/21.10/fqcleanerbiotools:fqcleaner0.4.1.1Web applicationhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_3572Data quality managementhttp://edamontology.org/topic_0080Sequence analysisgalaxyPasteurInstitut PasteurfqtoolsMatureOpen accesshttp://edamontology.org/operation_3192Sequence trimminghttp://edamontology.org/operation_3695Data filteringhttp://edamontology.org/data_0006Datahttp://edamontology.org/format_1930FASTQhttp://edamontology.org/data_0006Datahttp://edamontology.org/format_1930FASTQhttp://edamontology.org/data_0006Datahttp://edamontology.org/format_1930FASTQhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1929FASTAhttps://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/odoppelt/fqcleaner/fqCleaner/0.4.1.1Galaxy service10.1093/nar/gkw343Other10.7490/f1000research.1114334.1OtherGalaxy Support Teamgalaxy@pasteur.frPersonPrimary contactETENLNCETENLNC (End-To-End-Novel-NonCoding) is a lncRNA identification and analysis frameworkhttps://github.com/EvolOMICS-TU/ETENLNCetenlncbiotools:etenlnc1.0Command-line toolhttp://edamontology.org/topic_0659Functional, regulatory and non-coding RNALinuxMacWindowsGPL-3.0EmergingFree of chargeOpen accesshttp://edamontology.org/operation_3219Read pre-processinghttp://edamontology.org/operation_3218Sequencing quality controlhttp://edamontology.org/operation_3258Transcriptome assemblyhttp://edamontology.org/operation_0415Nucleic acid feature detectionhttp://edamontology.org/operation_3800RNA-Seq quantificationhttp://edamontology.org/operation_3223Differential gene expression profilinghttp://edamontology.org/operation_0531Heat map generationhttp://edamontology.org/operation_0278RNA secondary structure predictionhttp://edamontology.org/operation_3472k-mer countinghttp://edamontology.org/operation_0389Protein-nucleic acid interaction analysishttp://edamontology.org/operation_3901RNA-binding protein predictionhttp://edamontology.org/operation_2437Gene regulatory network predictionhttp://edamontology.org/data_2603Expression datahttp://edamontology.org/format_1930FASTQhttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1288Genome maphttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_3002Annotation trackhttp://edamontology.org/format_2306GTFhttp://edamontology.org/format_2305GFFRun ETENLNC on paired-end raw RNA-Seq (.fastq) databash ETENLNC_docker.shhttps://github.com/EvolOMICS-TU/ETENLNCRepositoryGitHub Repohttps://zenodo.org/records/14325721?token=eyJhbGciOiJIUzUxMiJ9.eyJpZCI6ImVmYTllNWJkLWE4ODUtNGM3OC05YTAxLWM4ZDk5YTljZDZjMCIsImRhdGEiOnt9LCJyYW5kb20iOiI4M2I1YjBlZDQ4MmUyZTIxNDg2YmI0YTFkMWE5MTI1OCJ9.HeB3WrsPduNzMyXjH4x5HfCgmIp4NzYv0P_11XU9lcXC_ZxEaVndP-kD0LDkxwufHVNlroeAhdK33PR51F6jnwBiological dataSample/demo data for ETENLNC. A detailed guide on running ETENLNC using the demo data can be found in the ETENLNC manual (supplementary to our publication).1.0https://github.com/EvolOMICS-TU/ETENLNCCommand-line optionsA detailed guide on running ETENLNC using the demo data can be found in the ETENLNC manual (supplementary to our publication)hisat2usessalmonusesfastqcusesfastpusesstringtieusesgffcompareusescpc2usesncbi_blast_plususestximportusesdeseq2useslnctarusescapsule-lpiusesseekruses10.1016/j.compbiolchem.2024.10814038996755Primary.0Pankaj Barahbarah@tezu.ernet.inhttps://www.tezu.ernet.in/dmbbt/profile/34https://orcid.org/0000-0001-7039-7996PersonPrimary contactMaintainerAssistant Professor at Department of Molecular Biology and Biotechnology, Tezpur University.Prangan Nathprangannathofficial@gmai.comhttps://orcid.org/0000-0002-9451-7822PersonDeveloperMaintainerUniversalMerUniversalMer is a k-mer counting tool for multiple size of k at once. It is available for DNA, RNA, and protein sequences. The program counts and summarizes the exact frequency of all k-mers from 1-mer to a user-defined maximum length (kmax). Analyzing the k-mer spectrum across multiple values of k can be done in seconds. This program is designed for bioinformatics researchers and scientists.https://ugrammer.github.ioUniversalMerbiotools:UniversalMer2.0.0Command-line toolhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_3473Data mininghttp://edamontology.org/topic_0080Sequence analysisWindowsMacC++CFreewareEmergingFree of chargeOpen accessToolsUKhttp://edamontology.org/operation_3472k-mer countinghttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_2546FASTA-likehttp://edamontology.org/data_3495RNA sequencehttp://edamontology.org/format_2546FASTA-likehttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_2546FASTA-likehttps://sourceforge.net/projects/universal-mer/Mirrorhttps://sourceforge.net/projects/universal-mer/Command-line specification2.0MirGeneDBMirGeneDB is a database of manually curated microRNA genes that have been validated and annotated as initially described in Fromm et al. 2015 , Fromm et al. 2020 and Fromm et al 2022. MirGeneDB 3.0 (Clarke and Hoye et al. 2024 ) includes more than 21,000 microRNA gene entries representing more than 1,700 microRNA families from 114 metazoan species. All microRNAs can be browsed, searched and downloaded.http://mirgenedb.org/mirgenbiotools:mirgen3.0doi:10.25504/FAIRsharing.QXSgvFdoi2.0Database portalhttp://edamontology.org/topic_0659Functional, regulatory and non-coding RNAhttp://edamontology.org/topic_0204Gene regulationhttp://edamontology.org/topic_3299Evolutionary biologyhttp://edamontology.org/topic_3500Zoologyhttp://edamontology.org/topic_2815Human biologyLinuxWindowsMacCC0-1.0UiO toolsELIXIR-NOELIXIR-NorwayMatureFree of chargeOpen accessNorwayhttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/data_1097Sequence accession (nucleic acid)http://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1869Organism identifierData retrieval: curated miRNA. Organism identifier: a specific miRNA identifier or a species for all miRNAs for that species. Gene transcript report: with metadata and visualization. RNA secondary structure: the hairpin loop of the miRNA with bases.http://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_1097Sequence accession (nucleic acid)https://elixir.no/helpdeskHelpdeskhttps://www.mirgenedb.org/downloadBiological dataSequence downloads for 75 species3.0https://www.mirgenedb.org/informationGeneral10.1093/nar/gkab110134850127PMC8728216Primary2.110.1093/nar/gkz88531598695PMC6943042Primary2.010.1146/annurev-genet-120213-09202326473382PMC4743252Primary1.010.1093/nar/gkae109439673268PMC11701709Primary3.0Bastian FrommBastianFromm@gmail.comhttps://orcid.org/0000-0003-0352-3037PersonPrimary contactDeveloperMaintainerSupportKevin J. Petersonkevin.j.peterson@dartmouth.eduPersonDeveloperMaintainerThe Norwegian Bioinformatics Platform (ELIXIR-Norway) Helpdesksupport@elixir.nohttps://elixir.no/helpdeskConsortiumSupportUniversity of Oslohttps://www.uio.no/english/index.htmlgrid.5510.101xtthb5610.13039/501100005366InstituteProviderRepeatModeler2RepeatModeler is a de novo transposable element (TE) family identification and modeling package. At the heart of RepeatModeler are three de-novo repeat finding programs ( RECON, RepeatScout and LtrHarvest/Ltr_retriever ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data.https://github.com/Dfam-consortium/RepeatModelerRepeatModeler2biotools:RepeatModeler22.0.7Command-line toolhttp://edamontology.org/topic_0621Model organismshttp://edamontology.org/topic_0157Sequence composition, complexity and repeatshttp://edamontology.org/topic_3673Whole genome sequencinghttp://edamontology.org/topic_0196Sequence assemblyhttp://edamontology.org/topic_0798Mobile genetic elementsMacLinuxPerlOSL-2.0MatureFree of chargehttp://edamontology.org/operation_0525Genome assemblyhttp://edamontology.org/operation_3644de Novo sequencinghttp://edamontology.org/operation_0362Genome annotationhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1929FASTAhttps://github.com/Dfam-consortium/RepeatModeler/blob/master/LICENSERepositoryrepeatmodelerisNewVersionOf10.1101/856591purge_dupsIdentifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuenceshttps://github.com/dfguan/purge_dupspurge_dupsbiotools:purge_dupsv.1.2.6http://edamontology.org/topic_0196Sequence assemblyMacLinuxPythonCMITONTeaterFree of chargeOpen accesshttp://edamontology.org/operation_0525Genome assemblyhttp://edamontology.org/operation_3798Read binninghttp://edamontology.org/operation_3216Scaffoldinghttp://edamontology.org/data_1234Sequence set (nucleic acid)http://edamontology.org/format_1930FASTQhttp://edamontology.org/data_1234Sequence set (nucleic acid)http://edamontology.org/format_1929FASTAhttps://github.com/dfguan/purge_dupsRepositoryhttps://github.com/dfguan/purge_dups/issuesIssue tracker10.1101/729962Dengfeng Guanhttps://www.chatlink.com.cnhttps://orcid.org/0000-0002-6376-3940PersonDeveloperCompleasmCompleasm: a faster and more accurate reimplementation of BUSCO.
It provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.https://github.com/huangnengCSU/compleasmcompleasmbiotools:compleasmv.0.2.5Command-line toolhttp://edamontology.org/topic_0196Sequence assemblyhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_0080Sequence analysisPythonApache-2.0ONTeaterMatureFree of chargeOpen accesshttp://edamontology.org/operation_3180Sequence assembly validationhttp://edamontology.org/data_1234Sequence set (nucleic acid)http://edamontology.org/format_2546FASTA-likeRuns compleasm using the BUSCO set corresponding to the lineage given.compleasm run -l "$lineage" -a assembly.fa -o output_prefixhttps://github.com/huangnengCSU/compleasmRepositoryhttps://github.com/huangnengCSU/compleasm/issuesIssue trackerhttps://busco.ezlab.org/list_of_lineages.htmlOtherList of accepted lineages (taxonomic groups with curated BUSCO sets)https://github.com/huangnengCSU/compleasm/blob/0.2.6/README.mdGeneralbuscoisNewVersionOf10.1093/bioinformatics/btad595Neng Huangneng@ds.dfci.harvard.eduhttps://orcid.org/0000-0001-7187-0749PersonDeveloperSILVA rRNA databaseSILVA provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukaryota).https://www.arb-silva.desilvabiotools:silvaRRID:SCR_006423rridWeb applicationDatabase portalhttp://edamontology.org/topic_0659Functional, regulatory and non-coding RNAhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3293Phylogeneticshttp://edamontology.org/topic_0637Taxonomyhttp://edamontology.org/topic_3050Biodiversityhttp://edamontology.org/topic_3301Microbiologyhttp://edamontology.org/topic_0632Probes and primersCC-BY-4.0de.NBIde.NBI-biodataDSMZ Digital DiversityMatureFree of chargeOpen accessDataGermanyhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_1097Sequence accession (nucleic acid)http://edamontology.org/format_1964plain text format (unformatted)http://edamontology.org/data_1868Taxonhttp://edamontology.org/format_1964plain text format (unformatted)http://edamontology.org/data_1046Strain namehttp://edamontology.org/format_1964plain text format (unformatted)http://edamontology.org/data_1088Article IDhttp://edamontology.org/format_1964plain text format (unformatted)http://edamontology.org/data_2909Organism namehttp://edamontology.org/format_1964plain text format (unformatted)The search and retrieval functions of the SILVA website can be used to build custom subsets of sequences. In addition to simple searches e.g. for accession numbers, organism names, taxonomic entities, or publication DOI/PubMed IDs, complex queries over several database fields using constraints such as sequence length or quality values are possible. The results can be sorted according to accession numbers, organism names, sequence length, sequence and alignment quality and Pintail values. The search results show accession number, organism name, sequence length, sequence quality values, taxonomic classifications, and links to view the full sequence record on SILVA and on ENA. Sequences found via search and added to download cart can be downloaded as FASTA and ARB files.http://edamontology.org/operation_2419Primer and probe designhttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1207nucleotidehttp://edamontology.org/data_1240PCR primershttp://edamontology.org/format_1207nucleotideThe SILVA Probe Match and Evaluation Tool detects and displays all occurrences of a given probe or primer sequence in the SILVA datasets.
TestPrime allows you to evaluate the performance of primer pairs by running an in silico PCR on the SILVA databases. From the results of the PCR, TestPrime computes coverages for each taxonomic group in all of the taxonomies offered by SILVA.http://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/operation_0496Global alignmenthttp://edamontology.org/operation_3460Taxonomic classificationhttp://edamontology.org/operation_0547Phylogenetic inference (maximum likelihood and Bayesian methods)http://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1984FASTA-alnThe Alignment, Classification and Tree Service (ACT) of SILVA allows to align and optionally classify sequences using the SILVA Incremental Aligner (SINA). From aligned sequences, (optionally) phylogenetic trees can be inferred using FastTree or RAxML.https://www.arb-silva.de/browser/ServiceSILVA Taxonomy Browserhttps://www.arb-silva.de/search/ServiceSILVA metadata searchhttps://www.arb-silva.de/aligner/ServiceACT: Alignment, Classification and Tree Servicehttps://www.arb-silva.de/search/testprobe/ServiceSILVA Probe Match and Evaluation Toolhttps://www.arb-silva.de/search/testprime/ServiceSILVA Primer Evaluation Toolhttps://treeviewer.arb-silva.de/ServiceWeb-based viewer for the SILVA guide treeshttps://www.arb-silva.de/download/archive/Downloads pageSILVA dataset archivehttps://www.arb-silva.de/silva-license-information/Terms of usehttps://www.arb-silva.de/contact/Citation instructionshttps://www.arb-silva.de/documentation/Generalhttps://www.arb-silva.de/documentation/faqs/FAQsilvangsusedByd3hubincludedIn10.1093/nar/gks121923193283PMC3531112Primary10.1093/nar/gkt120924293649PMC3965112Other10.1093/nar/gkm86417947321PMC2175337Other10.1093/bioinformatics/bts25222556368PMC3389763Other10.1016/j.jbiotec.2017.06.119828648396Review10.1186/s12859-017-1841-3OtherLeibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultureshub@dsmz.dehttps://www.dsmz.degrid.420081.f02tyer376InstituteProviderSILVA Teamcontact@arb-silva.dehttps://www.arb-silva.de/contact/team/grid.507782.f027z9pz32DivisionPrimary contactSILVAngsSILVAngs is a data analysis service for ribosomal RNA gene (rDNA) amplicon reads from high-throughput sequencing (next-generation sequencing (NGS)) approaches based on an automatic software pipeline. It uses the SILVA rDNA databases, taxonomies, and alignments as a reference. It facilitates the classification of rDNA reads and provides a wealth of results (tables, graphs and sequence files) for download.https://ngs.arb-silva.desilvangsbiotools:silvangs1.9.10Web applicationhttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/topic_3050Biodiversityhttp://edamontology.org/topic_0637Taxonomyhttp://edamontology.org/topic_0659Functional, regulatory and non-coding RNAhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3697Microbial ecologyde.NBIde.NBI-biodataDSMZ Digital DiversityMatureFree of charge (with restrictions)DataGermanyhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/operation_2478Nucleic acid sequence analysishttp://edamontology.org/operation_3460Taxonomic classificationhttp://edamontology.org/operation_2428Validationhttp://edamontology.org/operation_0291Sequence clusteringhttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1929FASTAThe pipeline accepts input data in Multi-Fasta format with each input file representing one sample. Samples that belong to one project (a transect, timeseries etc.) should be uploaded as a single SILVAngs project.https://www.arb-silva.de/fileadmin/silva_databases/sngs/SILVAngs_User_Guide.pdfUser manualhttps://www.arb-silva.de/documentation/silvangs/userfaq/FAQhttps://www.arb-silva.de/footer/sngs-termsofuseTerms of usesilvauses10.1093/nar/gks121923193283PMC3531112Primary10.1093/nar/gkt120924293649PMC3965112Primary10.1093/bioinformatics/bts25222556368PMC3389763PrimarySILVA Teamngs-contact@arb-silva.dehttps://www.arb-silva.de/contact/team/grid.507782.f027z9pz32DivisionPrimary contactLeibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultureshub@dsmz.dehttps://www.dsmz.degrid.420081.f02tyer376InstituteProviderDeepSigPrediction of secretory signal peptides in protein sequenceshttps://busca.biocomp.unibo.it/deepsig/deepsigbiotools:deepsig1.2.5Web applicationCommand-line toolhttp://edamontology.org/topic_3307Computational biologyhttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_0123Protein propertiesLinuxWindowsMacPythonC++GPL-3.0Bologna Biocomputing GroupMatureFree of chargeOpen accessItalyhttp://edamontology.org/operation_0418Protein signal peptide detectionhttp://edamontology.org/data_2974Protein sequence (raw)http://edamontology.org/format_1929FASTAhttp://edamontology.org/data_3028Taxonomyhttp://edamontology.org/format_2330Textual formathttps://github.com/BolognaBiocomp/deepsigSource code1.2.5https://hub.docker.com/r/bolognabiocomp/deepsigContainer file1.2.5https://github.com/BolognaBiocomp/deepsigCommand-line options10.1093/bioinformatics/btx81829280997PMC5946842Primary1.0ELIXIR-ITA-BOLOGNAhttp://biocomp.unibo.itInstituteProviderCastrense Savojardocastrense.savojardo2@unibo.ithttps://orcid.org/0000-0002-7359-0633PersonDeveloperPrimary contactPier Luigi Martellipierluigi.martelli@unibo.ithttp://biocomp.unibo.ithttps://orcid.org/0000-0002-0274-5669PersonPrimary contactNanoPlotNanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Bioscienceshttps://github.com/wdecoster/NanoPlotnanoplotbiotools:nanoplotv.1.42.0Command-line toolWeb applicationhttp://edamontology.org/topic_0622GenomicsMacLinuxWindowsPythonGPL-3.0ONTeaterMatureFree of charge (with restrictions)Open access (with restrictions)http://edamontology.org/operation_2940Scatter plot plottinghttp://edamontology.org/operation_2943Box-Whisker plot plottinghttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_2546FASTA-likehttp://edamontology.org/format_1207nucleotidehttps://github.com/wdecoster/NanoPlotRepositoryIssue tracker and most up to date software versionhttp://nanoplot.bioinf.be/ServiceWeb service with more limited options compared to the command line toolhttps://anaconda.org/bioconda/nanoplotCommand-line specificationhttps://pypi.org/project/NanoPlot/Command-line specificationhttps://github.com/wdecoster/NanoPlotCommand-line optionsnanopackincludedIn10.1093/bioinformatics/bty14929547981PMC6061794MethodWouter De Costerhttps://gigabaseorgigabyte.wordpress.com/https://orcid.org/0000-0002-5248-8197PersonDeveloperNextDenovoNextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a "correct-then-assemble" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages.https://github.com/Nextomics/NextDenovonextdenovobiotools:nextdenovov.2.5.2Command-line toolhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0196Sequence assemblyPythonCGPL-3.0ONTeaterMatureFree of chargeOpen accesshttp://edamontology.org/operation_0524De-novo assemblyhttp://edamontology.org/operation_0525Genome assemblyhttp://edamontology.org/data_0924Sequence tracehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1930FASTQhttps://github.com/Nextomics/NextDenovo/issuesIssue trackerhttps://github.com/Nextomics/NextDenovo/releases/tag/2.5.2Source codehttps://nextdenovo.readthedocs.io/en/latest/User manual10.1101/2023.03.09.531669.Nextomicssupport@nextomics.orgInstitutePrimary contactquickmergeQuickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.https://github.com/mahulchak/quickmergequickmergebiotools:quickmergev.0.3Command-line toolhttp://edamontology.org/topic_3175Structural variationhttp://edamontology.org/topic_0196Sequence assemblyhttp://edamontology.org/topic_2885DNA polymorphismhttp://edamontology.org/topic_3673Whole genome sequencinghttp://edamontology.org/topic_0625Genotype and phenotypeMacLinuxC++CGPL-3.0ONTeaterFree of chargeOpen accesshttp://edamontology.org/operation_0525Genome assemblyhttp://edamontology.org/operation_3216Scaffoldinghttp://edamontology.org/operation_0524De-novo assemblyhttp://edamontology.org/operation_3196Genotypinghttp://edamontology.org/data_1234Sequence set (nucleic acid)http://edamontology.org/format_1929FASTARuns whole merge process on an input assembly.
Assembly 2 will be used to fill gaps in assembly 1.merge_wrapper.py -pre output_prefix assembly_1.fa assembly_2.fahttps://github.com/mahulchak/quickmerge/issuesIssue trackerhttps://github.com/mahulchak/quickmergeRepository10.1534/g3.118.20016230018084PMC6169397PrimaryMahul Chakrabortyhttps://mahulchakraborty.wordpress.com/https://orcid.org/0000-0003-2414-9187PersonPrimary contactRaconConsensus module for raw de novo DNA assembly of long uncorrected reads
Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.https://github.com/isovic/raconRaconbiotools:Raconhttp://edamontology.org/topic_3673Whole genome sequencinghttp://edamontology.org/topic_0196Sequence assemblyMacLinuxC++PythonMITONTeaterFree of chargeOpen accesshttp://edamontology.org/operation_0525Genome assemblyhttp://edamontology.org/operation_0523Mapping assemblyhttp://edamontology.org/data_1383Nucleic acid sequence alignmenthttp://edamontology.org/format_2572BAMhttp://edamontology.org/format_2573SAMhttp://edamontology.org/data_1234Sequence set (nucleic acid)http://edamontology.org/format_1930FASTQhttp://edamontology.org/data_1234Sequence set (nucleic acid)http://edamontology.org/format_1929FASTA# The mapping file can be generated with any mapping program - eg, bwa-mem or minimap2.
# The following is an example using minimap2 with ONT data
minimap2 assembly.fa-ax map-ont reads.fa > mapped_reads.samracon -u reads.fa mapped_reads.sam assembly.fa > assembly_racon.fahttps://github.com/isovic/raconRepositoryhttps://github.com/isovic/racon/issuesIssue tracker10.3390/plants808027031390788PMC6724115Chon-Sik Kangcskang@korea.krPersonChangsoo Kimchangsookim@cnu.ac.krhttps://orcid.org/0000-0002-3596-2934PersonFlyeFlye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.https://github.com/fenderglass/FlyeFlyebiotools:Flye2.9.6Command-line toolWorkflowhttp://edamontology.org/topic_0196Sequence assemblyhttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/topic_3673Whole genome sequencinghttp://edamontology.org/topic_0622GenomicsMacLinuxC++PythonCBSD-3-ClauseONTeaterFree of chargeOpen accesshttp://edamontology.org/operation_0525Genome assemblyhttp://edamontology.org/operation_0524De-novo assemblyhttp://edamontology.org/operation_0523Mapping assemblyhttp://edamontology.org/operation_3730Cross-assemblyhttp://edamontology.org/data_1234Sequence set (nucleic acid)http://edamontology.org/format_1930FASTQhttps://github.com/fenderglass/Flye/issuesIssue trackerhttps://github.com/mikolmogorov/FlyeRepository10.1099/mgen.0.00029431483244PMC6807382Usage10.1038/s41587-019-0072-830936562Primary10.1038/s41592-020-00971-x33020656PMC10699202PrimaryMikhail Kolmogorovfenderglass@gmail.comPersonDeveloperSupportYu LinPersonDeveloperJeffrey YuanPersonDeveloperBUSCOProvides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.https://busco.ezlab.org/buscobiotools:busco1Command-line toolhttp://edamontology.org/topic_0196Sequence assemblyhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_0080Sequence analysisLinuxPythonToolsSwitzerlandhttp://edamontology.org/operation_3180Sequence assembly validationhttp://edamontology.org/data_1234Sequence set (nucleic acid)http://edamontology.org/format_1929FASTAhttps://busco.ezlab.org/busco_userguide.htmlUser manual10.1093/bioinformatics/btv3512605971710.1002/cpz1.3233493622110.1093/molbev/msx31929220515PMC585027810.1093/molbev/msab19934320186PMC8476166SIB Swiss Institute of BioinformaticsInstituteProviderevgeny.zdobnov@unige.chPersonPrimary contact