Workflows

MultiQC17 SAMtools13 Cutadapt9 fastp9 gfastats8 BEDTools6 Bowtie 26 BUSCO5 BWA5 lofreq5 MACS5 Minimap25 snpEff5 Bandage4 BCFtools4 GenomeScope 2.04 ggplot24 iVar4 kraken24 Merqury4 QualiMap4 Gromacs3 ToolDistillator3 AmberTools2 Cufflinks2 Medaka2 Open Babel2 purge_dups2 RDKit2 STAR2 ABRicate1 Bakta1 BamTools1 BLAST1 Bracken1 Bwa-mem21 bx-python1 ChemicalToolbox1 Clair31 Clustal 2 (Clustal W, Clustal X)1 compute_sequence_length1 FastQC1 FastTree1 Flye1 FreeBayes1 Integron Finder1 ISEScan1 KrakenTools1 NanoPlot1 Newick Utilities1 nextstrain.org1 PlasmidFinder1 QUAST1 Recentrifuge1 SeqCode1 shovill1 SRA Software Toolkit1 StringTie1 SuCOS1 taxonomy_krona_chart1 Vcflib1 More...

Galaxy93 Nextflow71

covid-198 Genomics8 Metagenomics8 rna8 rna-seq8 covid19.galaxyproject.org6 nanopore6 Assembly5 ChIP5 Proteomics5 single-cell5 variant-calling5 ABRomics4 ARTIC4 bacterial-genomics4 FASTQ4 illumina4 microbiome4 openms4 10x-genomics3 10xgenomics3 Annotation3 ATAC-seq3 denovo-assembly3 DNA3 image-processing3 mass-spectrometry3 Metabolomics3 RNASEQ3 taxonomic-classification3 taxonomic-profiling3 Transcriptomics3 adna2 AMR2 antibiotic-resistance2 antimicrobial-resistance-genes2 ChIP-seq2 demultiplexing2 differential-expression2 eDNA2 fasta2 GATK42 genome-assembly2 GTN2 Hi-C2 iwc2 long-read-sequencing2 long-reads2 Metabarcoding2 MS2 nanopore-sequencing2 NGS2 ONT2 paired-end2 peak-calling2 proteogenomics2 quality2 quantification2 Reviewed2 shotgun2 spatial2 star-solo2 taxonomy-assignment2 transcriptome2 vgp2 Virus2 workflow4metabolomics2 #single-cell1 16S1 18S1 airr1 alevin1 Alignment1 alphafold21 alternative-splicing1 amp1 Amplicon1 amplicon-sequencing1 ampliconarchitect1 ampliconsuite1 AMR-detection1 ancient-dna1 ancient-dna-analysis1 ancientdna1 antimicrobial resistance1 antimicrobial-peptides1 arg1 atac1 ATACseq1 b-cell1 bacteria1 bacterial1 bacterial-genome-analysis1 bacterial-genomes1 bamtofastq1 bases2fastq1 bcl2fastq1 bgc1 binning1 biosynthetic-gene-clusters1 bisulfite-sequencing1 bustools1 BWA-mem1 bwa-mem21 BY-COVID1 cage1 cage-seq1 cageseq-data1 cancer1 Cellranger1 chimeric-alignment1 chromatin-accessibiity1 chromatin-immunoprecipitation1 chromosome-conformation-capture1 circle-seq1 circular1 Classification1 clip1 clip-seq1 comparative-genomics1 Consensus1 contigs1 Conversion1 coprolite1 cosmic1 covid191 cramtofastq1 crispr1 crispr-analysis1 crispr-cas1 ctat1 cutandrun1 cutandrun-seq1 cutandtag1 cutandtag-seq1 CUTnRUN1 cytometry1 data-independent-proteomics1 ddbj1 de-identification1 decontamination1 deep-variant1 demo1 denovo1 deseq21 dia1 dia-proteomics1 diagnostics1 differential-abundance1 dna-methylation1 dot-plot1 download1 dualrna-seq1 eccdna1 ecdna1 elementbiosciences1 em-seq1 emergen_validated1 ena1 epigenome1 Epigenomics1 epitope1 epitope-prediction1 eukaryotes1 evolution1 evolutionary-tree1 extrachromosomal-circular-dna1 facs-sorting1 FastQC1 filter1 fish1 function1 fusion1 fusion-genes1 GC-MS1 gene-expression1 gene-fusion1 generic1 genome1 genome-annotation1 genomics-visualization1 geo1 Germline1 ggbio1 gnomad1 google1 gro-seq1 gsea1 HiC1 hicar1 hla1 hla-typing1 horizontal-gene-transfer1 host-pathogen1 hybrid-assembly1 identification1 image-analysis1 image-segmentation1 imaging1 immcantation1 immunology1 immunorepertoire1 iontorrent1 isoseq1 isoseq-31 ITS1 k-mer1 kallisto1 kmer1 kmer-counting1 kmer-frequency-count1 kraken21 krona1 label-free-quantification1 last1 LC-MS1 lfq1 limma1 linked-reads1 macs21 mapping1 MARS-seq1 mass-spec1 metagenomes1 metaMS1 metatranscriptomics1 methyl-seq1 mhc1 mhc-binding-prediction1 microarray1 microscopy1 minimal-example1 mnase-seq1 molecular-pixelation1 molecularcartography1 mpxv1 ms11 ms21 Multi-omics1 MultiQC1 name:amplicon1 name:single-cell1 nanostring1 nanostringnorm1 nascent1 natural-products1 nucleosome1 nucleosome-maps1 nucleosome-positioning1 optitype1 oxford-nanopore1 pacbio1 pairwise-alignment1 pangenome1 pathogen1 pathogen-genomics1 pbat1 peptides1 personalized-medicine1 phylogenetic-placement1 phylogenetics1 phylogeny1 pixelator1 pixelgen-technologies1 population-genetics1 pox1 pre-processing1 pro-seq1 Profiling1 prokaryotes1 protein-databases1 protein-fold-prediction1 protein-folding1 protein-sequences1 protein-structure1 proteins1 pypgatk1 QC1 qiime21 quantseq1 rare-disease1 readmapping1 repseq1 rna-rbp-interactions1 rrbs1 rrna1 SAMTools1 SARS-CoV-21 screening1 secondary-metabolites1 Segmentation1 sequence-classification1 shiny1 short-reads1 single-cell-omics1 single-cell-rna-seq1 slamseq1 small-rna1 smrna-seq1 snv1 Somatic1 spatial-transcriptomics1 splicing1 sra1 st1 structural-variants1 Supernova1 synapse1 synteny1 tama1 target-panels1 taxonomies1 tidyverse1 tmt1 training1 transcription1 transcriptional-dynamics1 tree1 trimming1 tss1 ultra1 umi1 umis1 unique-molecular-identifier1 variant-annotation1 viral1 viral-integration1 Virology1 viruses1 virusintegrationfinder1 visium1 wes1 WGS1 whole-exome-sequencing1 whole-genome-alignment1 whole-genome-sequencing1 worflow1 xcms1 More...

WorkflowHub Bot164

nf-core71 Intergalactic Workflow Commission (IWC)63 iwc30

nf-core71

Pierre Marin4 Clea Siguret3 Wolfgang Maier2 Wolfgang Maier1 Delphine Lariviere1

Freely accessible ready to use global infrastructure and workflows for SARS-CoV-2 monitoring6 Vertebrate Genomes Pipelines (VGP) workflows1 BY-COVID related workflows1

Deprecated4 Work-in-progress1 Stable1

Passing74 Not available9 All failing5