ProteinorthoProteinortho is a tool to detect orthologous genes within different specieshttps://gitlab.com/paulklemm_PHD/proteinorthoproteinorthobiotools:proteinortho6.3.1Command-line toolWorkflowhttp://edamontology.org/topic_0797Comparative genomicsLinuxMacWindowsPerlC++PythonGPL-2.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_0291Sequence clusteringhttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2048Reporthttp://edamontology.org/format_3475TSVhttp://edamontology.org/format_2331HTMLhttp://edamontology.org/format_2332XMLproteinortho input/*.faahttps://gitlab.com/paulklemm_PHD/proteinorthoRepositoryhttps://gitlab.com/paulklemm_PHD/proteinortho/-/issues?sort=created_date&state=openedIssue trackerhttps://toolshed.g2.bx.psu.edu/repository?repository_id=584d8accff31aefeGalaxy servicehttps://gitlab.com/paulklemm_PHD/proteinortho/-/archive/master/proteinortho-master.zipSource codeDownload and unpack, compile with `make all`latesthttps://packages.debian.org/unstable/proteinorthoDownloads pageInstallation with dpkg (root privileges are required)https://anaconda.org/bioconda/proteinorthoDownloads pageconda install proteinorthohttps://formulae.brew.sh/formula/proteinorthoDownloads pagebrew install proteinorthohttps://gitlab.com/paulklemm_PHD/proteinortho/-/releasesRelease noteshttps://gitlab.com/paulklemm_PHD/proteinortho/-/wikis/homeFAQhttps://gitlab.com/paulklemm_PHD/proteinorthoGeneralDiamondusesBLASTuses10.3389/fbinf.2023.1322477Primaryversion 6For the version 6 of proteinortho10.1186/1471-2105-12-12421526987PMC3114741version 4 to 5For version 4 to 5 of proteinortho10.1371/journal.pone.0105015OtherThe synteny extension PoFF (-syteny option)Marcus LechnerPersonPrimary contactMaintainerPaul Klemmhttps://gitlab.com/paulklemmhttps://orcid.org/0000-0002-3609-5713PersonMaintainerHIV-TRACEHIV-TRACE is an application that identifies potential transmission clusters within a supplied FASTA file.https://github.com/veg/hivtracehiv-tracebiotools:hiv-trace0.1.7JavaScriptMITMatureFree of chargeOpen accesshttp://edamontology.org/operation_0004Operationhttp://edamontology.org/data_3495RNA sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2042Evidencehttp://edamontology.org/format_3464JSONhttps://github.com/veg/hivtrace?tab=readme-ov-fileIssue trackerhttps://github.com/veg/hivtrace/archive/refs/tags/0.7.1.zipSource code0.1.7GetMLSTdownloads MLST datasets from pubmlst.orghttps://github.com/katholt/srst2getmlstbiotools:getmlst0.2.0PerlBSD-2-ClauseMatureFree of chargeOpen accesshttps://github.com/katholt/srst2Issue trackerhttps://github.com/katholt/srst2/archive/refs/tags/v0.2.0.zipDownloads page0.2.0nonpareilEstimate metagenomic coverage and sequence diversityhttp://enve-omics.ce.gatech.edu/nonpareil/nonpareilbiotools:nonpareil3.4.1Artistic-2.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_0004Operationhttp://edamontology.org/data_3495RNA sequencehttp://edamontology.org/format_1930FASTQhttp://edamontology.org/data_2042Evidencehttp://edamontology.org/format_3475TSVnonpareil -s reads.fa -T kmer -f fastq -b output # fastq is recommended for kmer algorithmhttps://github.com/lmrodriguezr/nonpareilIssue trackerhttps://github.com/lmrodriguezr/nonpareil/archive/refs/tags/v3.4.1.zipSource code3.4.1https://nonpareil.readthedocs.ioGeneral10.1093/bioinformatics/btt584Luis M Rodriguez-Rmiguel@rodriguez-r.comhttps://github.com/lmrodriguezrPersonDeveloperoncoanalyserOncoanalyser is an nf-core Nextflow implementation of the tools developed by Hartwig Medical Foundation. The workflow is designed to comprehensively detect all variant types (SNV. MNV, InDel, SV, CNV, Fusions, Viral insertions, Telomere length, Genetic Immune Escape, mutational processes) as well as key tumor characteristics (purity, ploidy, TMB, MSI) from data derived from different short read platforms. The tooling is optimised for paired whole genome samples (90x tumor, 30x normal) but can be run on exome or panel (targeted) data. There is support for GRCh37 and GRCh38 human reference genome builds.https://github.com/nf-core/oncoanalyser/tree/devoncoanalyserbiotools:oncoanalyser5.34Workflowhttp://edamontology.org/topic_2640Oncologyhttp://edamontology.org/topic_3673Whole genome sequencinghttp://edamontology.org/topic_3170RNA-SeqLinuxWindowsMacJavaGPL-3.0MatureFree of chargeOpen accesshttps://github.com/nf-core/oncoanalyser/tree/devIssue trackerRepositoryGitHub page for issue tracking of Nextflow workflow implementationhttps://github.com/hartwigmedical/hmftoolsRepositoryIssue trackerGitHub repository of underlying tools with issue trackinghictkBlazing fast toolkit to work with .hic and .cool fileshttps://github.com/paulsengroup/hictkhictkbiotools:hictk0.0.10.0.20.0.30.0.40.0.50.0.60.0.70.0.80.0.90.0.10Command-line toolhttp://edamontology.org/topic_0091BioinformaticsLinuxMacWindowsMIThttps://github.com/paulsengroup/hictkRepositoryhttps://github.com/paulsengroup/hictk/issuesIssue trackerhttps://github.com/paulsengroup/hictk/releasesDownloads pagehttps://anaconda.org/bioconda/hictkBinarieshttps://github.com/paulsengroup/hictk/pkgs/container/hictkContainer filehttps://hictk.readthedocs.io/en/latest/index.htmlUser manual10.1101/2023.11.26.568707PrimaryM2aiaM²aia (MSI applications for interactive analysis in MITK) is a software tool enabling interactive signal processing and visualisation of mass spectrometry imaging (MSI) datasets. M²aia extends the open source Medical Imaging and Interaction Toolkit (MITK; https://www.mitk.org) and provides powerful methods that the MSI community can adopt, exploit and improve further. In it’s current state, it is designed to enable multi-modal 2D registration and 3D MSI reconstruction.https://m2aia.github.io/m2aiam2aiabiotools:m2aiaRRID:SCR_019324rridDesktop applicationCommand-line toolhttp://edamontology.org/topic_0091BioinformaticsLinuxWindowsC++BSD-3-ClauseEmergingFree of chargeOpen accesshttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3682imzML metadata filehttp://edamontology.org/format_3839ibdhttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3551nrrdhttp://edamontology.org/format_3727OME-TIFFhttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3682imzML metadata filehttp://edamontology.org/format_3839ibdhttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3551nrrdhttps://github.com/m2aia/m2aiaIssue trackerRepositoryhttps://www.mitk.orgOtherhttps://m2aia.deDownloads pagehttps://www.protocols.io/view/supporting-protocol-for-use-case-1-dimensionality-brw4m7gwTraining materialSupporting protocol for use-case 1: Dimensionality reduction in "M2aia - Interactive, fast and memory efficient analysis of 2D and 3D multi-modal mass spectrometry imaging data"https://www.protocols.io/view/supporting-protocol-for-use-case-2-multi-modal-3d-bvq8n5zwTraining materialSupporting protocol for use-case 2: Multi-modal 3D image reconstruction in "M2aia - Interactive, fast and memory efficient analysis of 2D and 3D multi-modal mass spectrometry imaging data"https://www.protocols.io/view/supporting-protocol-for-use-case-1-n-linked-glycan-bvq5n5y6Training materialSupporting protocol for use-case 1: N-linked glycan m/z candidate detection in "M2aia - Interactive, fast and memory efficient analysis of 2D and 3D multi-modal mass spectrometry imaging data"https://doi.org/10.24433/CO.2384502.v1Training materialSupporting capsule for use-case 1: R-based processing in "M²aia - Interactive, fast and memory efficient analysis of 2D and 3D multi-modal mass spectrometry imaging data"https://doi.org/10.24433/CO.7662658.v1Training materialSupporting capsule for use-case 1: Command-line application based pre-processing in "M²aia - Interactive, fast and memory efficient analysis of 2D and 3D multi-modal mass spectrometry imaging data"MALVIRUSMALVIRUS is a fast and accurate tool for genotyping haploid individuals that does not require to assemble the read nor mapping them to a reference genome. It is tailored to work with virological data and can genotype an individual directly from sequencing data in minutes. MALVIRUS is divided into two logically distinct steps: the creation of a variant catalog from a set of assemblies and the genotype calling. The first step is based on mafft and snp-sites, whereas the second step is based on KMC and MALVA. The variant catalog can be built once and reused for genotyping multiple individuals. Please see the website for additional details. MALVIRUS is distributed as a Docker image and is publicly available on GitHub and Docker Hub under the terms of the GNU General Public License version 3 or later. MALVIRUS was mainly developed and tested under Ubuntu GNU/Linux version 18.04 but works wherever Docker is available.https://algolab.github.io/MALVIRUSmalvirusbiotools:malvirus3.0.1Web applicationDesktop applicationhttp://edamontology.org/topic_0781Virologyhttp://edamontology.org/topic_3796Population genomicsLinuxWindowsMacGPL-3.0COVID-19EmergingFree of chargeOpen accessItalyhttp://edamontology.org/operation_0484SNP detectionhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_3002Annotation trackhttp://edamontology.org/format_2305GFFhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1930FASTQhttp://edamontology.org/data_3498Sequence variationshttp://edamontology.org/format_3016VCFhttps://github.com/AlgoLab/MALVIRUSRepositoryhttps://github.com/AlgoLab/MALVIRUS/issuesIssue trackerhttps://hub.docker.com/r/algolab/malvirusContainer filehttps://algolab.github.io/MALVIRUS/USAGEUser manual10.1186/s12859-022-04668-0Primary10.1101/2020.05.05.076992PrimaryYuri Pirolayuri.pirola@unimib.ithttps://algolab.eu/pirolahttps://orcid.org/0000-0002-8479-7592PersonMaintainerELIXIR-ITA-BICOCCAInstituteSharkFast tool for mapping-free gene separation of reads, using Bloom filter.https://github.com/AlgoLab/sharkSharkbiotools:Shark1.2.0Command-line toolhttp://edamontology.org/topic_3170RNA-SeqLinuxC++GPL-3.0EmergingFree of chargeItalyhttp://edamontology.org/operation_3695Filteringhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_3495RNA sequencehttp://edamontology.org/format_1930FASTQhttp://edamontology.org/data_3495RNA sequencehttp://edamontology.org/format_1930FASTQhttps://github.com/AlgoLab/sharkRepositoryhttps://github.com/AlgoLab/shark/issuesIssue trackerhttps://github.com/AlgoLab/shark/releasesDownloads page10.1093/bioinformatics/btaa779Primary10.1101/836130OtherYuri Pirolayuri.pirola@unimib.ithttps://algolab.eu/pirolahttps://orcid.org/0000-0002-8479-7592PersonELIXIR-ITA-BICOCCAInstituteMETA-pipeMETA-pipe is a Nextflow workflow designed for comprehensive annotation and in-depth exploration of marine metagenomics samples. META-pipe offers insight into the phylogenetic diversity, metabolic capabilities, and functional potential of these environmental communities. The workflow is divided into four modules: read processing (merging, filtering, 16S rRNA extraction, assembly), taxonomic classification using reads against RefSeq/MAR databases and predicted 16S rRNA, binning, and functional assignment of predicted coding sequences (CDSs).https://mmp2.sfb.uit.no/metapipe/meta-pipebiotools:meta-pipe1.0.01.1.0 - 1.1.21.2.01.3.0 - 1.3.2WorkflowWeb applicationhttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/topic_0736Protein folds and structural domainshttp://edamontology.org/topic_3512Gene transcriptshttp://edamontology.org/topic_3387Marine biologyhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0637Taxonomyhttp://edamontology.org/topic_0085Functional genomicsLinuxWindowsMacGroovyMITELIXIR-NOELIXIR-NorwayUiTMMPMatureFree of chargeOpen access (with restrictions)ToolsMarine MetagenomicsNorwayhttp://edamontology.org/operation_3921Sequence read processinghttp://edamontology.org/operation_3460Taxonomic classificationhttp://edamontology.org/operation_3798Read binninghttp://edamontology.org/operation_2478Nucleic acid sequence analysishttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1930FASTQhttp://edamontology.org/data_0925Sequence assemblyhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2884Plothttp://edamontology.org/format_2331HTMLhttp://edamontology.org/data_3002Annotation trackhttp://edamontology.org/format_2305GFFhttp://edamontology.org/data_2048Reporthttp://edamontology.org/format_1957rawIf you execute META-pipe yourself, the raw output of all tools are accessible. Through the web service, the main outputs are: assembly (FASTA), Krona visualization (HTML), gene annotations (GFF), MAGs, and the raw outputs of some of the tools.https://mmp2.sfb.uit.no/metapipe-service/ServiceMETA-pipe's web interface, requires LS AAI or ELIXIR login.https://gitlab.com/uit-sfb/metapipeIssue trackerRepositoryhttps://elixir.no/helpdeskHelpdeskHelpdesk and support for ELIXIR Norway services.https://gitlab.com/uit-sfb/metapipe/-/releases/1.3.2Source codeLatest release as of 9 August 2023.1.3.2https://gitlab.com/uit-sfb/metapipe/-/releasesDownloads pageAll releases.https://gitlab.com/uit-sfb/metapipe/-/wikis/homeCommand-line optionsGeneralInstallation instructionsQuick start guidehttps://gitlab.com/uit-sfb/metapipe/-/wikis/Workflow/OverviewGeneralmmpincludedIn10.48550/arXiv.1604.04103PrimaryThe Norwegian Bioinformatics Platform (ELIXIR-Norway) Helpdesksupport@elixir.nohttps://elixir.no/helpdeskConsortiumPrimary contactSupportErik Hjerdeerik.hjerde@uit.nohttps://orcid.org/0000-0002-6014-1249PersonContributorIgor Molchanovigor.molchanov@uit.nohttps://orcid.org/0000-0003-4252-2387PersonDeveloperEspen Robertsenhttps://orcid.org/0000-0003-2752-6224PersonDeveloperMayeul Marcadellamayeul.marcadella@gmail.comhttps://orcid.org/0000-0001-8555-3808PersonDeveloperDocumentorTim Kahlkehttps://orcid.org/0000-0002-9762-6573PersonDeveloperEdvard PedersenPersonDeveloperInge Alexander RaknesPersonDeveloperNils-Peder Willassenhttps://orcid.org/0000-0002-4397-8020PersonContributorUiT The Arctic University of Norwayhttps://en.uit.no/grid.10919.3000wge5k7810.13039/100007465InstituteProvider