All Published Workflows

Pathway ID (KEGG) Quantification Quality control report prodigal MEGAHIT BEDTools BWA cd-hit Diamond fastp kallisto MMseqs Quant SAMtools seqtk Snakemake subSeq kofam_scan oschmod metagenomics

raw sequence reads Quantification Quality control report BWA FastQC gffread GFFutils HTSeq htseqcount kallisto MultiQC QualiMap Quant RSEM Salmon SAMtools Snakemake STAR Trim_Galore Gene expression

FASTQ Data Quantification Quality control report PCAtools tximport apeglm Cutadapt DESeq2 FastQC MultiQC pheatmap Quant regionReport Salmon sleuth Snakemake vsn ggplot2 readr stringr RNA-Seq

Gene ID Quantification Gene report gffread SAMtools Snakemake RNA-Seq

Quantification bracken kraken2 seqtk Snakemake sourmash ggplot2 Sequence analysis

JSON Quantification Barrnap BBMap BEDTools BLAST gffread Pandas Quant Salmon Snakemake matplotlib RNA-Seq

JSON Quantification Variant calling tabix BEDTools Biopython CAT Pandas Pybedtools RTG Core SAMtools Snakemake ggplot2 ggpubr infotheo tidyverse common more-itertools numpy PyYAML sklearn typing-extensions Genomics

Quantification bracken kraken2 seqtk Snakemake sourmash ggplot2 Genomics

Expression analysis Quantification AdapterRemoval FastQC Quant Salmon SAMtools Snakemake Gene expression

Gene ID Nextflow Quantification Alignment Nextflow Pandas Pyteomics Snakemake networkx numpy Gene structure

Quantification IPO Nextflow Data quality management

FASTQ-illumina raw sequence reads Quantification genetic variants ABRicate FastQC kallisto metaprokka Minimap2 MMseqs Nextflow Quant SAMtools TransDecoder metagenomics