Workflows

European Nucleotide Archive (ENA)1 FastQC45 MultiQC30 SAMtools24 SCANPY22 Cutadapt16 QUAST16 ggplot215 Bowtie 214 BWA14 BEDTools13 BUSCO13 fastp13 scikit-learn13 Bandage12 JBrowse12 FreeBayes11 Minimap211 mothur11 MaxQuant10 msConvert10 BamTools9 DropletUtils9 HISAT29 kraken29 BCFtools8 DeepTools8 NanoPlot8 seqtk8 STAR8 Trimmomatic8 BLAST7 Flye7 MACS7 StringTie7 taxonomy_krona_chart7 Trim Galore7 Biopython6 FeatureCounts6 gffcompare6 Open Babel6 RSeQC6 Unipept6 UniProt6 COMBAT-TB Workbench5 DESeq25 Galactic Circos5 GEMINI5 gffread5 Merqury5 Prokka5 Salmon5 Unicycler5 annotatemyids4 bed to protein map4 Bwa-mem24 bx-python4 customProDB4 epiScanpy4 Galaxy Image Analysis4 GenomeScope 2.04 KrakenTools4 MEGAHIT4 metaQuantome4 MSstatsTMT4 snippy4 SRA Software Toolkit4 Stacks4 anndata3 Bracken3 Cardinal3 Clustal 2 (Clustal W, Clustal X)3 GOseq3 Gromacs3 HUMAnN23 InterProScan (EBI)3 MetaPhlAn3 MSstats3 MuSiC Deconvolution3 Newick Utilities3 MuSiC suite: PoPMuSiC, HoTMuSiC, and SNPMuSiC3 pyGenomeTracks3 Racon3 scikit-image3 tb-profiler3 UMI-tools3 Bakta2 Bio3D2 BioRuby2 CellProfiler2 ChEMBL2 chemfp2 compute_sequence_length2 cshl_fastx_reverse_complement2 Diamond2 diaPASEF2 eggNOG-mapper v22 FastTree2 FlashLFQ2 funannotate2 gfastats2 GOEnrichment2 humann2 limma2 lofreq2 MAFFT2 MAKER2 MDAnalysis2 Medaka2 MEME2 MetaNovo2 metaspades2 mzToSQLite2 NGSUtils2 The Protein Data Bank (PDB)2 pilon2 purge_dups2 QIIME2 R2 RAxML2 RDKit2 Recentrifuge2 RepeatMasker2 SALSA2 SeqCode2 Seurat2 snpEff2 staramr2 tbl2gff32 Vcflib2 WoLF PSORT2 Workflow4Metabolomics2 xcms2 ABRicate1 AmberTools1 antiSMASH1 Apollo1 AUGUSTUS1 blockbuster1 Bowtie1 ChemicalToolbox1 ChIPpeakAnno1 ChiRA1 Circos1 Clair31 clusterProfiler1 dada21 edgeR1 EGA1 EGSEA1 ewastools1 export2graphlan1 Falco1 FASTX-Toolkit1 FEELnc1 fgsea1 Filtlong1 FREEC1 GAEVAL1 Galaxy1 GATK1 GECKO1 g:Profiler1 GraPhlAn1 Heinz1 Helixer1 HiCExplorer1 The Immune Epitope Database (IEDB)1 Integron Finder1 iqtree1 ISEScan1 IsoformSwitchAnalyzeR1 IWTomics1 Krona1 LASTZ1 lotus21 MAGeCK1 MALDIquant1 Matchms1 MethylDackel1 miniasm1 miRDeep21 NCBI Resources1 Nextflow1 OBITools1 OMArk1 OptiType1 pangolin1 pathview1 Peakachu1 PfamScan1 phyloseq1 PlasFlow1 PlasmidFinder1 Polypolish1 Prodigal1 Proteinortho1 PYLFIRE1 pymethylprocess1 QualiMap1 RaceID1 RAMClustR1 RapidNJ1 RCAS1 RED1 RIAssigner1 rnaQUAST1 scater1 Seq2HLA1 shovill1 Smudgeplots1 SNAP1 SortMeRNA1 SPAdes1 SuCOS1 Targetfinder.org1 TransDecoder1 TRANSIT1 Trinity1 Trinotate1 VarScan1 VelvetOptimiser1 More...

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