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: http://dx.doi.org/10.1101/012179

Comprehensive interpretation of human genome sequencing data is a challenging bioinformatic problem that typically requires weeks of analysis, with extensive hands-on expert involvement. This informatics bottleneck inflates genome sequencing costs, poses a computational burden for large-scale projects, and impedes the adoption of time-critical clinical applications such as personalized cancer profiling and newborn disease diagnosis, where the actionable timeframe can measure in hours or days. We developed SpeedSeq, an open-source genome analysis platform that vastly reduces computing time. SpeedSeq accomplishes read alignment, duplicate removal, variant detection and functional annotation of a 50X human genome in <24 hours, even using one low-cost server. SpeedSeq offers competitive or superior performance to current methods for detecting germline and somatic single nucleotide variants (SNVs), indels, and structural variants (SVs) and includes novel functionality for SV genotyping, SV annotation, fusion gene detection, and rapid identification of actionable mutations. SpeedSeq will help bring timely genome analysis into the clinical realm.