Sentieon DNA pipeline for variant detection - Software-only solution, over 20× faster than GATK 3.3 with identical results

Jessica A. Weber; Rafael Aldana; Brendan D. Gallagher; Jeremy S. Edwards

doi:10.7287/peerj.preprints.1672v2

Sentieon DNA pipeline for variant detection - Software-only solution, over 20× faster than GATK 3.3 with identical results

Jessica A. Weber¹, Rafael Aldana ², Brendan D. Gallagher², Jeremy S. Edwards^3,4,5

1 Department of Biology, University of New Mexico, Albuquerque, NM, USA

2 Sentieon Inc., Mountain View, CA, USA

3 Department of Chemistry & Chemical Biology, University of New Mexico, Albuquerque, NM, USA

4 Department of Molecular Genetics and Microbiology, University of New Mexico, Albuquerque, NM, USA

5 Department of Chemical & Nuclear Engineering, University of New Mexico, Albuquerque, NM, USA

DOI: 10.7287/peerj.preprints.1672v2

Published: 2016-01-22
Accepted: 2016-01-22

Subject Areas: Bioinformatics, Genomics
Keywords: DNA sequencing, Bioinformatics

Copyright: © 2016 Weber et al.
Licence: This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.

Cite this article: Weber JA, Aldana R, Gallagher BD, Edwards JS. 2016. Sentieon DNA pipeline for variant detection - Software-only solution, over 20× faster than GATK 3.3 with identical results. PeerJ PrePrints 4:e1672v2 https://doi.org/10.7287/peerj.preprints.1672v2

Abstract

Sentieon DNAseq Software is a suite of tools for running DNA sequencing secondary analyses. The Sentieon DNAseq Software produces identical results to the Genome Analysis Toolkit (GATK) Best Practice Workflow using HaplotypeCaller, with more than a 20-fold increase in processing speed on the same hardware.

This paper presents a benchmark analysis of the GATK and Sentieon DNAseq software packages using publically available datasets from the 1000 genomes database, and includes speed comparisons and output concordance analyses.