Workflows

MaxBin1 MultiQC36 fastp31 SAMtools31 BUSCO24 BWA21 Minimap221 FastQC17 gfastats15 BEDTools14 Merqury13 BLAST12 Bowtie 212 Cutadapt11 kraken211 Bandage10 BCFtools10 Bwa-mem29 SRA Software Toolkit9 GenomeScope 2.08 taxonomy_krona_chart8 lofreq7 MaBoSS7 MACS7 PhysiCell7 QUAST7 SCANPY7 Galaxy6 gffread6 ggplot26 purge_dups6 seqtk6 shovill6 StringTie6 FASTX-Toolkit5 Flye5 Konstanz Information Miner (KNIME)5 QualiMap5 R5 snpEff5 Stacks5 TransDecoder5 Trimmomatic5 UniProt5 antiSMASH4 Cufflinks4 NanoPlot4 Racon4 RepeatMasker4 Seurat4 SPAdes4 STAR4 Unicycler4 anndata3 Biopython3 bx-python3 cisTEM3 DESeq23 Gromacs3 HISAT23 Infernal3 iqtree3 iVar3 MAPseq3 Medaka3 MotionCor23 Nextflow3 Open Babel3 picard_samtofastq3 PretextView3 RDKit3 Scipion3 ToolDistillator3 Vcflib3 Variant Effect Predictor (VEP)3 ABRicate2 AmberTools2 BamTools2 BBMap2 biomformat2 Bracken2 BRAKER12 CellProfiler2 ChiRA2 CNVkit2 Diamond2 FreeBayes2 funannotate2 GATK2 HiCExplorer2 JBrowse2 KrakenTools2 MAFFT2 MaxQuant2 nanopolish2 NCBI Datasets2 NGSUtils2 OMArk2 Picard2 PredPrIn2 PRINSEQ2 RepeatModeler2 RSeQC2 Smudgeplots2 Snakemake2 SnpSift2 tophat22 VADR2 vardict2 VarScan2 vcfanno2 vcfutils2 VSEARCH2 XMIPP2 YaHS2 AdapterRemoval1 AGAT1 ampvis1 AnnotSV1 Bioconductor1 BioContainers1 BlobToolKit1 CARNIVAL1 cBioPortal1 CheckM1 ChemicalToolbox1 Clair31 Clustal 2 (Clustal W, Clustal X)1 Clustal 1.8 (Clustal W, Clustal X)1 clusterProfiler1 cmsearch-deoverlap1 COMBAT-TB Workbench1 compute_sequence_length1 cuffdiff1 decoupleR1 DeepTools1 DeepVariant1 Delly21 edgeR1 EGA1 eggNOG-mapper v21 EMBOSS1 FastTree1 FEELnc1 FGENESH1 Filtlong1 FLASH1 Foldseek1 GADES1 Galaxy Image Analysis1 gblocks1 GBMatch - GBMPredictor1 GEMINI1 GetOrganelle1 ggtree1 GOseq1 GSEA1 hAMRonization1 Helixer1 HiFiAdapterFilt1 Hifiasm1 htseqcount1 HTSlib1 ImageJ21 Integron Finder1 InterProScan (EBI)1 ISEScan1 JBrowse 21 MAKER1 Mash1 Matchms1 Meryl1 MetaBAT 21 MetaNovo1 miniasm1 miniprot1 MitoHiFi1 MITOS1 MOB-suite1 MolMeDB1 Metagenomic operational taxonomic units (mOTUs)1 msConvert1 MSMetaEnhancer1 MSstats1 MUMmer1 Newick Utilities1 ngsReports1 OBITools1 PEAR1 PhysiBoSS1 pilon1 PlasmidFinder1 PLINK1 Prodigal1 progeny1 Proteinortho1 protexcluder1 pyfastaq1 Recentrifuge1 recetox-msfinder1 RepeatModeler1 scikit-image1 SemiBin1 SeqCode1 seqkit1 SeqSero21 SISTR1 snipit1 snippy1 staramr1 Subread1 SuCOS1 tabix1 TaxonKit1 tb-profiler1 Trim Galore1 UCSC Genome Browser Utilities1 Unipept1 VAPOR1 varlociraptor1 WGCNA1 More...

Common Workflow Language1

Assembly1 binning1 illumina1 Metagenomics1

Bart Nijsse1

UNLOCK1

Independent Teams1

Jasper Koehorst1 Bart Nijsse1 Changlin Ke1

Bioinformatics1 Metagenomic sequencing1 Metagenomics1 Sequence assembly1

Sequence assembly1

Work-in-progress1