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

Research output: Contribution to journalArticle

140 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 languageEnglish
Pages (from-to)966-968
Number of pages3
JournalNature Methods
Volume12
Issue number10
DOIs
StatePublished - Sep 29 2015

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    Chiang, C., Layer, R. M., Faust, G. G., Lindberg, M. R., Rose, D. B., Garrison, E. P., Marth, G. T., Quinlan, A. R., & Hall, I. M. (2015). SpeedSeq: Ultra-fast personal genome analysis and interpretation. Nature Methods, 12(10), 966-968. https://doi.org/10.1038/nmeth.3505