All Published Workflows

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

GTF Text data Methylation analysis Plot nanopolish Snakemake nanopore

Database ID Taxonomic classification Plot bracken kraken-biom cmapR ALDEx2 Kraken kraken2 Krona Pandas Snakemake ggplot2 ggpubr RColorBrewer reshape2 vegan metagenomics

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

bacterial Labeled quantification Scatter plot plotting Plot bracken kraken2 Pandas Snakemake stringr numpy metagenomics

bigWig Sample annotation cis-regulatory element prediction Plot cooltools Snakemake Data architecture, analysis and design

Sequence similarity FASTQ Homology-based gene prediction Plot dlcpar hmmer hmmer2 BLAST BLAST (EBI) BTOD HMMER3 HMMER hmmscan (EBI) HMMER phmmer (EBI) OrthoFinder SMI-BLAST Snakemake Comparative genomics

Sample annotation Filtering Plot delly sniffles AnnotSV BCFtools BWA FastQC Picard Samplot SAMtools Snakemake TIDDIT SURVIVOR Trim_Galore Structural variation

Genome index Genome analysis Plot pheatmap Snakemake ggplot2 ggplotify viridis gene similarity analysis

TSV paired sequencing data Expression analysis Filtering Plot BEDTools Biopython Bowtie 2 Pandas SAMtools Snakemake intervaltree matplotlib networkx numpy pysam scipy seaborn De Novo

JSON Gene tree Sequence mutation and randomisation Plot Biopython Pandas Snakemake matplotlib numpy DNA mutation

raw sequence reads Genome assembly Plot nanofilt Biopython BWA fastp FastQC Flye Medaka Pandas Snakemake Unicycler Genomics