SpeedSeq: ultra-fast personal genome analysis and interpretation

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.

Figure 1. SpeedSeq workflow

(a) SpeedSeq converts raw reads into prioritized variants in 13 hours for a 50× human dataset. (b) Germline SNV (N=2,803,144) and (c) indel (N=364,031) receiver operating characteristic (ROC) curves over the Genome in a Bottle (GIAB) truth set for SpeedSeq, GATK Unified Genotyper (GATK-UG) and Haplotype Caller (GATK-HC). (d) Somatic SNV detection ROC curves for a simulated 50× tumor-normal pair using SpeedSeq and three other tools (N=875,206). Open circles (b-d) denote the data points reported in the main text. (e) SpeedSeq’s SV detection performance by quality score of all SVs (black), those with split-read and paired-end support (blue), and those with read-depth support from CNVnator (red), as validated by either PacBio/Moleculo long-reads or the 1000 Genomes Project. (f) Schematic of haplotype-based SV validation showing undetected (open circles), consistently segregating (black circles), and inconsistently segregating (red circles) SVs through the CEPH 1463 pedigree.

Figure 2. Case study in a tumor-normal pair

A SpeedSeq workflow demonstrating the seven succinct commands required to process a tumor-normal pair (TCGA-E2-A14P) from raw FASTQ reads to clinically actionable somatic mutations with predicted damaging consequences. In this tumor, SpeedSeq detected a previously reported somatic gene fusion product between exon 1 of TBL1XR1 and exon 2 of PIK3CA.