All Published Workflows

raw sequence reads Read pre-processing Report umi_tools BBMap Biopython Cutadapt FastQC MultiQC Seurat Snakemake STAR devtools dplyr ggplot2 gridExtra Matrix plotly plyr RColorBrewer stringr tidyr viridis yaml pysam scRNAseq data processing

Sample annotation Sequencing quality control Report Augur BEDTools Pangolin SAMtools Snakemake Genomics

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

Data Read pre-processing Report Biostrings BSgenome BWA Quant SAMtools Snakemake magrittr DNA

Feature table Analysis Report eukrep prodigal MEGAHIT BWA CoverM FastQC MetaBAT 2 MultiQC SAMtools Snakemake Trimmomatic CONCOCT metagenomics

Data Analysis Report BWA SAMBLASTER SAMtools Snakemake Data identity and mapping

Data Analysis Report Quant Salmon Seurat SingleCellExperiment Snakemake devtools ggplot2 Matrix rjson pybiomart Data quality management

Data index Analysis Report FastANI MMseqs NanoPlot SAMtools seqkit Snakemake Molecular evolution

Peptide ID Cross-assembly Report Pandas Snakemake broom yaml altair more-itertools numpy PyYAML scipy peptide

Sample annotation Analysis Report bracken FastQC humann kraken2 MultiQC seqkit Snakemake metagenomics

TSV Sample annotation Genetic mapping Report tabix BCFtools mosdepth Sambamba Snakemake snpEff Trim_Galore Genetic variation

Sample annotation Sequencing quality control Report rust-bio-tools snakemake-wrapper-utils BCFtools Pandas SAMtools Snakemake Varlociraptor nanopore