plasmidspadesGenome assembler for plasmids.http://cab.spbu.ru/software/spades/plasmidspadesbiotools:plasmidspades3.9.0Web applicationhttp://edamontology.org/topic_0196Sequence assemblyhttp://edamontology.org/topic_0622GenomicsLinuxWindowsMacgalaxyPasteurSPAdesMatureOpen accesshttp://edamontology.org/operation_0525Genome assemblyhttp://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_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_1929FASTAhttp://edamontology.org/data_0006Datahttp://edamontology.org/format_1930FASTQhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0006Datahttp://edamontology.org/format_1930FASTQhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0006Datahttp://edamontology.org/format_1930FASTQhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0006Datahttp://edamontology.org/format_3475TSVhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0006Datahttp://edamontology.org/format_3475TSVhttp://edamontology.org/data_0006Datahttp://edamontology.org/format_2330Textual formathttps://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/plasmidspades/plasmidspades/3.9.0Galaxy servicehttp://spades.bioinf.spbau.ru/release3.11.1/manual.html#plasmidGeneral10.1089/cmb.2012.0021Primary10.1093/nar/gkw343Other10.7490/f1000research.1114334.1OtherGalaxy Support Teamgalaxy@pasteur.frPersonPrimary contactrnaspadesPipeline for de novo transcriptome assembly from RNA-Seq.http://cab.spbu.ru/software/spades/rnaspadesbiotools:rnaspades3.9.0RRID:SCR_016992rridWeb applicationhttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_3168SequencingLinuxWindowsMacgalaxyPasteurSPAdesMatureOpen accesshttp://edamontology.org/operation_0524De-novo assemblyhttp://edamontology.org/operation_3258Transcriptome assemblyhttp://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_1929FASTAhttp://edamontology.org/data_0006Datahttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_0006Datahttp://edamontology.org/format_2330Textual formathttps://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/rnaspades/rnaspades/3.9.0Galaxy servicehttp://spades.bioinf.spbau.ru/release3.11.1/rnaspades_manual.htmlUser manual10.1089/cmb.2012.0021Primary10.1093/nar/gkw343Other10.7490/f1000research.1114334.1OtherGalaxy Support Teamgalaxy@pasteur.frPersonPrimary contactmetaspadesGenome assembler for metagenomics datasets.http://cab.spbu.ru/software/spades/metaspadesbiotools:metaspades3.9.0Web applicationhttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacPythongalaxyPasteurSPAdesMatureOpen accesshttp://edamontology.org/operation_3182Genome alignmenthttp://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_1929FASTAhttp://edamontology.org/data_0006Datahttp://edamontology.org/format_3475TSVhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0006Datahttp://edamontology.org/format_3475TSVhttp://edamontology.org/data_0006Datahttp://edamontology.org/format_2330Textual formathttps://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/metaspades/metaspades/3.9.0Galaxy servicehttp://spades.bioinf.spbau.ru/release3.11.1/manual.htmlUser manual10.1089/cmb.2012.0021Primary10.1093/nar/gkw343Other10.7490/f1000research.1114334.1OtherGalaxy Support Teamgalaxy@pasteur.frPersonPrimary contactSPAdesSt. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.http://cab.spbu.ru/software/spades/spadesbiotools:spadesCommand-line toolhttp://edamontology.org/topic_0196Sequence assemblyLinuxMacPythonGPL-2.0SPAdesgalaxyPasteurAnimal and Crop GenomicsMatureOpen accesshttp://edamontology.org/operation_0525Genome assemblyhttp://edamontology.org/data_0006Datahttp://edamontology.org/format_1930FASTQhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0006Datahttp://edamontology.org/format_3475TSVhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0006Datahttp://edamontology.org/format_3475TSVhttp://edamontology.org/data_0006Datahttp://edamontology.org/format_2330Textual formathttps://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/spades/spades/3.9.0Galaxy servicehttp://cab.spbu.ru/files/release3.10.1/manual.htmlUser manual10.1089/cmb.2012.0021Primary10.7490/f1000research.1114334.1Otherspades.support@cab.spbu.ruPersonPrimary contactRiboGalaxyGalaxy-based web server where researchers can pre-process, align, analyze and visualize their own ribosome profiling (ribo-seq) data. GUI-based tools are provided to determine the strength of the triplet periodicity signal in ribo-seq data, generate metagene and ribosome profiles and carry out differential translation expression analysis using the riboSeqR suite. The RUST suite of tools can be used to quickly characterize ribosome profiling datasets to assess their quality and more.http://ribogalaxy.ucc.ieribogalaxybiotools:ribogalaxy1Workbenchhttp://edamontology.org/topic_0203Gene expressionWindowsMacMatureFree of chargeGalaxyhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_2928Alignmenthttp://edamontology.org/operation_0314Gene expression profilinghttp://edamontology.org/operation_2495Gene expression analysishttp://edamontology.org/data_0848Raw sequencehttp://edamontology.org/format_1932FASTQ-sangerhttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3603PNGhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_2572BAMhttp://edamontology.org/format_3006bigWighttp://edamontology.org/data_2969Sequence imagehttp://edamontology.org/format_3603PNGRaw ribo-seq and mRNA-seq FASTQ files There are multiple outputs depending on the tool/jobs that are run. Most of the ribo-seq analysis tools provide the output in both spreadsheet and/or visual format.https://github.com/riboseqorg/RiboGalaxyRepositoryhttp://ribogalaxy.ucc.ie/static/conditions_of_use.htmlTerms of usehttp://ribogalaxy.ucc.ie/General10.1080/15476286.2016.114186226821742PMC4829337Primary10.1016/J.JMB.2023.16804337356899ReviewScience Foundation Irelandinfo@sfi.ieFunding agencyContributorucc.iehttp://www.ucc.ieInstituteProviderribogalaxy@gmail.comhttp://ribogalaxy.ucc.ie/PersonPrimary contactPavel V. Baranovp.baranov@ucc.ieHMMER hmmscan (EBI)HMMER3 hmmscan is used to search sequences against collections of profiles.https://www.ebi.ac.uk/jdispatcher/pfa/hmmer3_hmmscanhmmer_hmmscan_ebibiotools:hmmer_hmmscan_ebi1Web applicationWeb servicehttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0160Sequence sites, features and motifshttp://edamontology.org/topic_0623Gene and protein familiesMacLinuxWindowsEBI ToolsJob Dispatcher Toolshttp://edamontology.org/operation_0338Sequence database searchhttp://edamontology.org/data_0849Sequence recordhttp://edamontology.org/data_1364Hidden Markov modelhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_2066Database hits (sequence) formathttp://edamontology.org/data_0857Sequence search resultshttps://www.ebi.ac.uk/about/contact/support/job-dispatcher-servicesHelpdeskhttp://hmmer.org/Downloads pagehttp://www.ebi.ac.uk/about/terms-of-useTerms of usehttps://www.ebi.ac.uk/jdispatcher/helpGeneralhttp://hmmer.org/Generalhmmer3uses10.1093/nar/gkr367Primary10.1093/nar/gkac240OtherSean EddyPersonDeveloperEMBL-EBIInstituteProviderJob Dispatcherhttps://www.ebi.ac.uk/jdispatcherProjectPrimary contactHMMER phmmer (EBI)HMMER3 phmmer is used to search one or more sequences against a sequence database.https://www.ebi.ac.uk/jdispatcher/pfa/hmmer3_phmmerhmmer_phmmer_ebibiotools:hmmer_phmmer_ebi1Web applicationWeb servicehttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0160Sequence sites, features and motifshttp://edamontology.org/topic_0623Gene and protein familiesMacLinuxWindowsEBI ToolsJob Dispatcher Toolshttp://edamontology.org/operation_0338Sequence database searchhttp://edamontology.org/data_0849Sequence recordhttp://edamontology.org/data_1364Hidden Markov modelhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_2066Database hits (sequence) formathttp://edamontology.org/data_0857Sequence search resultshttps://www.ebi.ac.uk/about/contact/support/job-dispatcher-servicesHelpdeskhttp://hmmer.org/Downloads pagehttp://www.ebi.ac.uk/about/terms-of-useTerms of usehttps://www.ebi.ac.uk/jdispatcher/helpGeneralhttp://hmmer.org/Generalhmmer3uses10.1093/nar/gkr367Primary10.1093/nar/gkac240OtherSean EddyPersonDeveloperEMBL-EBIInstituteProviderJob Dispatcherhttps://www.ebi.ac.uk/jdispatcherProjectPrimary contactseqret (EBI)Sequence format coversion tool.https://www.ebi.ac.uk/jdispatcher/sfc/emboss_seqretseqret-ebibiotools:seqret-ebi1Web applicationWeb servicehttp://edamontology.org/topic_3071Data managementLinuxWindowsMacEMBOSS at EBI ToolsEBI ToolsJob Dispatcher Toolshttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_0335Formattinghttp://edamontology.org/data_2044Sequencehttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/data_2044Sequencehttp://edamontology.org/data_0863Sequence alignmenthttps://www.ebi.ac.uk/about/contact/support/job-dispatcher-servicesHelpdeskhttps://emboss.sourceforge.net/Downloads pagehttp://www.ebi.ac.uk/about/terms-of-useTerms of usehttps://www.ebi.ac.uk/jdispatcher/helpGeneralhttps://emboss.sourceforge.net/Generalseqretuses10.1016/S0168-9525(00)02024-2Primary10.1093/nar/gkac240OtherEMBOSSPersonDeveloperEMBL-EBIInstituteProviderJob Dispatcherhttps://www.ebi.ac.uk/jdispatcherProjectPrimary contactMView (EBI)Reformat the results of a sequence database search (BLAST, FASTA) or a multiple alignment adding optional HTML markup to control colouring and web page layout.https://www.ebi.ac.uk/jdispatcher/msa/mviewmview_ebibiotools:mview_ebi1Web applicationWeb servicehttp://edamontology.org/topic_3071Data managementhttp://edamontology.org/topic_0092Data visualisationLinuxWindowsMacEBI ToolsJob Dispatcher Toolshttp://edamontology.org/operation_0335Formattinghttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1948nbrf/pirhttp://edamontology.org/format_1982ClustalW formathttp://edamontology.org/data_0857Sequence search resultshttp://edamontology.org/format_1948nbrf/pirhttp://edamontology.org/format_1982ClustalW formathttp://edamontology.org/data_0863Sequence alignmenthttps://www.ebi.ac.uk/about/contact/support/job-dispatcher-servicesHelpdeskhttps://desmid.github.io/mview/Downloads pagehttp://www.ebi.ac.uk/about/terms-of-useTerms of usehttps://www.ebi.ac.uk/jdispatcher/helpGeneralhttps://desmid.github.io/mview/General10.1093/bioinformatics/14.4.380Primary10.1093/nar/gkac240OtherNigel BrownPersonDeveloperEMBL-EBIInstituteProviderJob Dispatcherhttps://www.ebi.ac.uk/jdispatcherProjectPrimary contactMUSCLE (EBI)Sequence alignment using the Multiple Sequence Comparison by Log-Expectation (MUSCLE) methodhttps://www.ebi.ac.uk/jdispatcher/msa/musclemuscle_ebibiotools:muscle_ebi1RRID:SCR_011812rridWeb applicationWeb servicehttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacMUSCLEEBI ToolsJob Dispatcher Toolshttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/data_2044Sequencehttp://edamontology.org/data_0863Sequence alignmenthttps://www.ebi.ac.uk/about/contact/support/job-dispatcher-servicesHelpdeskhttps://www.drive5.com/muscle/Downloads pagehttp://www.ebi.ac.uk/about/terms-of-useTerms of usehttps://www.ebi.ac.uk/jdispatcher/helpGeneralhttps://www.drive5.com/muscle/Generalmuscleuses10.1093/nar/gkh340Primary10.1093/nar/gkac240OtherRobert EdgarPersonDeveloperEMBL-EBIInstituteProviderJob Dispatcherhttps://www.ebi.ac.uk/jdispatcherProjectPrimary contact