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Sarek :
Sarek : A portable workflow for whole-genome sequencing analysis of germline and somatic variants
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Nystedt, B. (författare)
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Garcia, M. (författare)
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Juhos, S. (författare)
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Larsson, M. (författare)
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Olason, P. I. (författare)
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Martin, M. (författare)
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Eisfeldt, J. (författare)
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DiLorenzo, S. (författare)
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Sandgren, J. (författare)
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Díaz De Ståhl, T. (författare)
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Ewels, P. (författare)
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Wirta, V. (författare)
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Nistér, M. (författare)
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- Käller, Max (författare)
- KTH,Science for Life Laboratory, SciLifeLab,Genteknologi
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(creator_code:org_t)
- 2020-01-29
- 2020
- Engelska.
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Ingår i: F1000 Research. - : F1000 Research Ltd. - 2046-1402. ; 9
- Relaterad länk:
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https://doi.org/10.1...
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https://f1000researc...
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
Ämnesord
Stäng
- Whole-genome sequencing (WGS) is a fundamental technology for research to advance precision medicine, but the limited availability of portable and user-friendly workflows for WGS analyses poses a major challenge for many research groups and hampers scientific progress. Here we present Sarek, an open-source workflow to detect germline variants and somatic mutations based on sequencing data from WGS, whole-exome sequencing (WES), or gene panels. Sarek features (i) easy installation, (ii) robust portability across different computer environments, (iii) comprehensive documentation, (iv) transparent and easy-to-read code, and (v) extensive quality metrics reporting. Sarek is implemented in the Nextflow workflow language and supports both Docker and Singularity containers as well as Conda environments, making it ideal for easy deployment on any POSIX-compatible computers and cloud compute environments. Sarek follows the GATK best-practice recommendations for read alignment and pre-processing, and includes a wide range of software for the identification and annotation of germline and somatic single-nucleotide variants, insertion and deletion variants, structural variants, tumour sample purity, and variations in ploidy and copy number. Sarek offers easy, efficient, and reproducible WGS analyses, and can readily be used both as a production workflow at sequencing facilities and as a powerful stand-alone tool for individual research groups. The Sarek source code, documentation and installation instructions are freely available at https://github.com/nf-core/sarek and at https://nf-co.re/sarek/.
Ämnesord
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
Nyckelord
- Analysis workflow
- Cancer
- Germline variants
- Somatic variants
- Whole Genome Sequencing
- access to information
- Article
- bioinformatics
- cloud computing
- genetic variability
- genome
- indel mutation
- information dissemination
- karyotyping
- quality control
- reproducibility
- single nucleotide polymorphism
- software
- workflow
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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Till lärosätets databas
- Av författaren/redakt...
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Nystedt, B.
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Garcia, M.
-
Juhos, S.
-
Larsson, M.
-
Olason, P. I.
-
Martin, M.
-
visa fler...
-
Eisfeldt, J.
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DiLorenzo, S.
-
Sandgren, J.
-
Díaz De Ståhl, T ...
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Ewels, P.
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Wirta, V.
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Nistér, M.
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Käller, Max
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visa färre...
- Om ämnet
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- NATURVETENSKAP
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NATURVETENSKAP
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och Biologi
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och Bioinformatik oc ...
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F1000 Research
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Kungliga Tekniska Högskolan