kerstenbreuer

Run cwltool with singularity-based containerization within Docker.

Container for deploying singularity inside docker (nested containerization).

Bismark aligner along with samtools and bowtie2.

bioconductor's clusterProfiler along with ReactomePA and reactome.db

deeptools

adapter trimmer

Fast and Accurate MEthylation Aligner (https://github.com/FischerJo/FAME)

Trimmomatic read trimmer.

bowtie2 mapper

samtools

toil runner with the CWL extras

bwameth optimized for sigularity

multiqc optimized for use with singularity

NucleoATAC optimized for use with singularity

bedGraphToBigWig from kent utilities for use with singularity.

Picard tools

Ubuntu-based container with the r meta-package tidyverse installed.

Downloader for raw reads (fastq) from the ENA database.

FastQC - quality control for NGS reads.

Megahit - an assembler for NGS reads.

Kraken tool used to taxonomically classify metagenomic sequences.

Bbmap / BBTools package.

Container for using SIAMCAT (https://git.embl.de/grp-zeller/SIAMCAT/).