SpeedSeq: ultra-fast personal genome analysis and interpretation.

Chiang C1, Layer RM2, Faust GG3, Lindberg MR3, Rose DB3, Garrison EP4, Marth GT2, Quinlan AR2, Hall IM5.

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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.