All Published Workflows

Database metadata Peak calling Plot macs2 BEDTools Bowtie 2 DeepTools FastQC MultiQC Sambamba SAMBLASTER SAMtools Snakemake ChIP-seq

JSON raw sequence reads Variant calling genetic variants delly gatk rust-bio-tools snakemake-wrapper-utils tabix BCFtools BEDTools Bowtie 2 BWA Cutadapt FastQC fgbio FreeBayes mosdepth MultiQC Pandas Picard SAMtools Snakemake Variant Effect Predictor (VEP) vembrane numpy oschmod sklearn statsmodels Varlociraptor DNA

Expression data Peak calling Plot macs2 ataqv BEDTools Bowtie 2 DeepTools FastQC MultiQC SAMBLASTER SAMtools Snakemake ATAC-seq

bracken prodigal Bowtie 2 Diamond kraken2 Snakemake VSEARCH

BAM Sample ID Mapping Report gatk tabix AdapterRemoval BCFtools BEDTools Bowtie 2 BWA fastp FastQC gatk_realigner_target_creator MapDamage MultiQC Pandas Picard QualiMap SAMtools seqtk Snakemake GLIMPSE numpy Comparative genomics

BSgenome.Hsapiens.UCSC.hg19 BSgenome.Hsapiens.UCSC.hg38 Gene ID Peak calling Quality control report macs2 ucsc-liftover BEDTools BiocParallel Bowtie 2 csaw Cufflinks GenomicAlignments GenomicRanges GLUE graphite GSEABase HISAT2 kallisto Quant rtracklayer Salmon SAMtools Snakemake SRAdb STAR SummarizedExperiment assertthat dplyr forcats future getopt ggforce ggplot2 here ks magrittr optparse reshape2 rex rlang scales stringr rpy2 rctutils ChIP-seq

JSON bracken BBMap Bowtie 2 fastp FeatureCounts humann Kaiju Kraken kraken2 KrakenUniq Krona MetaPhlAn MultiQC Pandas SAMtools Singularity Hub Snakemake matplotlib numpy seaborn

raw sequence reads Analysis Sequence report scp MEGAHIT Anvio BEDTools Bowtie 2 Centrifuge FastQC HUMAnN2 Kraken Mash MetaQUAST MultiQC Pandas QUAST SAMtools seqtk Snakemake SPAdes SqueezeMeta numpy scikit-bio Sequence analysis

Barrnap prodigal MEGAHIT Biopython BLAST Bowtie 2 Centrifuge CheckM contigtax Cutadapt edgeR eggNOG-mapper v2 FastANI FastQC FeatureCounts Infernal cmscan (EBI) kraken2 Krona MaxBin MetaBAT 2 metagenomeSeq MetaPhlAn metaspades MultiQC Pandas Picard SAMtools seqtk Snakemake SortMeRNA SqueezeMeta Trimmomatic Trnascan-SE CONCOCT common gtdbtk networkx numpy RGI

pmdtools AMPS Bowtie 2 Cutadapt FastQC KrakenUniq Krona MapDamage MultiQC SAMtools seqtk Snakemake subSeq Malt

preseq ucsc-bigwigmerge ucsc-bigwigtobedgraph PCAtools bedGraphToBigWig BEDTools Bowtie 2 Consensus DeepTools DESeq2 fastp FastQC MultiQC Pandas pheatmap plyranges Sambamba SAMtools Snakemake vsn dendextend ggplot2 ggrepel gplots PoiClaClu RColorBrewer tidyr tidyverse plotly

scp Bowtie 2 BWA CheckM CRIMSON dRep FastQC Mash metaprokka MetaWRAP MultiQC SAMtools seqtk Snakemake SPAdes SRA ggplot2 gridExtra RColorBrewer tidyr gtdbtk