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nf-core/sarek is a workflow designed to detect variants on whole genome or targeted sequencing data. Initially designed for Human, and Mouse, it can work on any species with a reference genome. Sarek can also handle tumour / normal pairs and could include additional relapses.

The pipeline is built usingNextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. TheNextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed fromnf-core/modules in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!

On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on thenf-core website.

It's listed onElixir - Tools and Data Services Registry andDockstore.

Depending on the options and samples provided, the pipeline can currently perform the following:

• Form consensus reads from UMI sequences (fgbio)
• Sequencing quality control and trimming (enabled by--trim_fastq) (FastQC,fastp)
• Map Reads to Reference (BWA-mem,BWA-mem2,dragmap orSentieon BWA-mem)
• Process BAM file (GATK MarkDuplicates,GATK BaseRecalibrator andGATK ApplyBQSR orSentieon LocusCollector andSentieon Dedup)
• Summarise alignment statistics (samtools stats,mosdepth)
• Variant calling (enabled by--tools, seecompatibility):
  • ASCAT
  • CNVkit
  • Control-FREEC
  • DeepVariant
  • freebayes
  • GATK HaplotypeCaller
  • Manta
  • indexcov
  • mpileup
  • MSIsensor-pro
  • Mutect2
  • Sentieon Haplotyper
  • Strelka2
  • TIDDIT
  • Lofreq
• Variant filtering and annotation (SnpEff,Ensembl VEP,BCFtools annotate)
• Summarise and represent QC (MultiQC)

First, prepare a samplesheet with your input data that looks as follows:

samplesheet.csv:

patient,sample,lane,fastq_1,fastq_2ID1,S1,L002,ID1_S1_L002_R1_001.fastq.gz,ID1_S1_L002_R2_001.fastq.gz

Each row represents a pair of fastq files (paired end).

Now, you can run the pipeline using:

nextflow run nf-core/sarek \   -profile<docker/singularity/.../institute> \   --input samplesheet.csv \   --outdir<OUTDIR>

For more details and further functionality, please refer to theusage documentation and theparameter documentation.

To see the results of an example test run with a full size dataset refer to theresults tab on the nf-core website pipeline page.For more details about the output files and reports, please refer to theoutput documentation.

On each release, the pipeline is run on 3 full size tests:

• test_full runs tumor-normal data for one patient from the SEQ2C consortium
• test_full_germline runs a WGS 30X Genome-in-a-Bottle(NA12878) dataset
• test_full_germline_ncbench_agilent runs two WES samples with 75M and 200M reads (data availablehere). The results are uploaded to Zenodo, evaluated against a truth dataset, and results are made available via theNCBench dashboard.

Sarek was originally written by Maxime U Garcia and Szilveszter Juhos at theNational Genomics Infastructure andNational Bioinformatics Infastructure Sweden which are both platforms atSciLifeLab, with the support ofThe Swedish Childhood Tumor Biobank (Barntumörbanken).Friederike Hanssen and Gisela Gabernet atQBiC later joined and helped with further development.

The Nextflow DSL2 conversion of the pipeline was lead by Friederike Hanssen and Maxime U Garcia.

Maintenance is now lead by Friederike Hanssen and Maxime U Garcia (now atSeqera Labs)

Main developers:

• Maxime U Garcia
• Friederike Hanssen

We thank the following people for their extensive assistance in the development of this pipeline:

• Abhinav Sharma
• Adam Talbot
• Adrian Lärkeryd
• Àitor Olivares
• Alexander Peltzer
• Alison Meynert
• Anders Sune Pedersen
• arontommi
• BarryDigby
• Bekir Ergüner
• bjornnystedt
• cgpu
• Chela James
• David Mas-Ponte
• Edmund Miller
• Famke Bäuerle
• Francesco Lescai
• Francisco Martínez
• Gavin Mackenzie
• Gisela Gabernet
• Grant Neilson
• gulfshores
• Harshil Patel
• Hongwei Ye
• James A. Fellows Yates
• Jesper Eisfeldt
• Johannes Alneberg
• José Fernández Navarro
• Júlia Mir Pedrol
• Ken Brewer
• Lasse Westergaard Folkersen
• Lucia Conde
• Malin Larsson
• Marcel Martin
• Nick Smith
• Nicolas Schcolnicov
• Nilesh Tawari
• Nils Homer
• Olga Botvinnik
• Oskar Wacker
• pallolason
• Paul Cantalupo
• Phil Ewels
• Pierre Lindenbaum
• Sabrina Krakau
• Sam Minot
• Sebastian-D
• Silvia Morini
• Simon Pearce
• Solenne Correard
• Susanne Jodoin
• Szilveszter Juhos
• Tobias Koch
• Winni Kretzschmar

If you would like to contribute to this pipeline, please see thecontributing guidelines.

For further information or help, don't hesitate to get in touch on theSlack#sarek channel (you can join withthis invite), or contact us:Maxime U Garcia,Friederike Hanssen

If you usenf-core/sarek for your analysis, please cite theSarek article as follows:

Friederike Hanssen, Maxime U Garcia, Lasse Folkersen, Anders Sune Pedersen, Francesco Lescai, Susanne Jodoin, Edmund Miller, Oskar Wacker, Nicholas Smith, nf-core community, Gisela Gabernet, Sven NahnsenScalable and efficient DNA sequencing analysis on different compute infrastructures aiding variant discoveryNAR Genomics and Bioinformatics Volume 6, Issue 2, June 2024, lqae031,doi: 10.1093/nargab/lqae031.

Garcia M, Juhos S, Larsson M et al.Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants [version 2; peer review: 2 approved]F1000Research 2020, 9:63doi: 10.12688/f1000research.16665.2.

You can cite the sarek zenodo record for a specific version using the followingdoi: 10.5281/zenodo.3476425

An extensive list of references for the tools used by the pipeline can be found in theCITATIONS.md file.

You can cite thenf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi:10.1038/s41587-020-0439-x.

• CHANGELOG