SpeedSeq: Ultra-fast personal genome analysis and interpretation

Colby Chiang; Ryan M. Layer; Gregory G. Faust; Michael R. Lindberg; David B. Rose; Erik P. Garrison; Gabor T. Marth; Aaron R. Quinlan; Ira M. Hall

doi:10.1038/nmeth.3505

SpeedSeq: Ultra-fast personal genome analysis and interpretation

Colby Chiang
, Ryan M. Layer
, Gregory G. Faust
, Michael R. Lindberg
, David B. Rose
, Erik P. Garrison
, Gabor T. Marth
, Aaron R. Quinlan
, Ira M. Hall

Section of Medical Oncology

Research output: Contribution to journal › Article › peer-review

418 Scopus citations

Abstract

SpeedSeq is an open-source genome analysis platform that accomplishes alignment, variant detection and functional annotation of a 50× human genome in 13 h on a low-cost server and alleviates a bioinformatics bottleneck that typically demands weeks of computation with extensive hands-on expert involvement. SpeedSeq offers performance competitive with or superior to current methods for detecting germline and somatic single-nucleotide variants, structural variants, insertions and deletions, and it includes novel functionality for streamlined interpretation.

Original language	English
Pages (from-to)	966-968
Number of pages	3
Journal	Nature Methods
Volume	12
Issue number	10
DOIs	https://doi.org/10.1038/nmeth.3505
State	Published - Sep 29 2015

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10.1038/nmeth.3505

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author = "Colby Chiang and Layer, \{Ryan M.\} and Faust, \{Gregory G.\} and Lindberg, \{Michael R.\} and Rose, \{David B.\} and Garrison, \{Erik P.\} and Marth, \{Gabor T.\} and Quinlan, \{Aaron R.\} and Hall, \{Ira M.\}",

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AU - Garrison, Erik P.

AU - Marth, Gabor T.

AU - Quinlan, Aaron R.

AU - Hall, Ira M.

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SpeedSeq: Ultra-fast personal genome analysis and interpretation

Abstract

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