Table 1. Software required and implemented in Sarek.

A list of all the software required and currently implemented in Sarek. All analysis and quality metrics software are installed automatically when Sarek is launched. P, Preprocessing; G, Germline; S, Somatic; snv, Single-nucleotide variants and small indels; sv, Structural variants; pp, Ploidy and sample purity; a, Annotation.

Software/Resource	Analyses	Availability
Required software
Nextflow		https://www.nextflow.io/index.html
Docker, Singularity or Conda		https://www.docker.com/, https://sylabs.io/, https://docs.conda.io/en/latest/
Included analysis software
BWA-MEM	P	http://bio-bwa.sourceforge.net/
GATK4	P, G(snv)	https://software.broadinstitute.org/gatk/
Samtools	P, G(snv)	https://github.com/samtools/samtools
Strelka2	G(snv), S(snv)	https://github.com/Illumina/strelka
Manta	G(sv), S(sv)	https://github.com/Illumina/manta
TIDDIT	G(sv)	https://github.com/SciLifeLab/TIDDIT
GATK4 Mutect2	S(snv)	https://gatk.broadinstitute.org/hc/en-us/articles/360037593851-Mutect2
Freebayes	S(snv)	https://github.com/ekg/freebayes
ASCAT	S(pp)	https://github.com/Crick-CancerGenomics/ascat
Control-FREEC	S(pp)	http://boevalab.inf.ethz.ch/FREEC/
snpEff	G(a), S(a)	http://snpeff.sourceforge.net/
VEP	G(a), S(a)	http://www.ensembl.org/vep
Included quality metrics software
MultiQC		http://multiqc.info/
FastQC		https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
BamQC		https://github.com/s-andrews/BamQC
QualiMap		http://qualimap.bioinfo.cipf.es/
BCFtools		https://github.com/samtools/bcftools
VCFtools		https://vcftools.github.io/index.html