BALSA - Integrated secondary analysis for whole-genome and whole-exome sequencing, accelerated by GPU

A new bioinformatics paper from Ruibang Luo? and others in Tak-Wah Lam’s group.

BALSA: Integrated secondary analysis for whole-genome and whole-exome sequencing, accelerated by GPU

This paper reports an integrated solution, called BALSA, for the secondary analysis of next generation sequencing data; it exploits the computational power of GPU and an intricate memory management to give a fast and accurate analysis. From raw reads to variants (including SNPs and Indels), BALSA, using just a single computing node with a commodity GPU board, takes 5.5 hours to process 50-fold whole genome sequencing (~750 million 100bp paired-end reads), or just 25 minutes for 210-fold whole exome sequencing. BALSAs speed is rooted at its parallel algorithms to effectively exploit a GPU to speed up processes like alignment, realignment and statistical testing. BALSA incorporates a 16-genotype model to support the calling of SNPs and Indels and achieves competitive variant calling accuracy and sensitivity when compared to the ensemble of six popular variant callers. BALSA also supports efficient identification of somatic SNVs and CNVs; experiments showed that BALSA recovers all the previously validated somatic SNVs and CNVs, and it is more sensitive for somatic Indel detection. BALSA outputs variants in VCF format. A pileup-like SNAPSHOT format, while maintaining the same fidelity as BAM in variant calling, enables efficient storage and indexing, and facilitates the App development of downstream analyses.

For previous work from the same group, please check -

GPU-Accelerated BWT Construction for Large Collection of Short Reads

SOAP3-dp: Fast, Accurate and Sensitive GPU-Based Short Read Aligner

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We just finished reading the paper and found the benchmarks quite impressive.

In summary, from raw reads to variants (including SNPs and Indels), BALSA finished in 5.49 hours, whereas ISAAC finished in 11.92 hours, and GATK coupled with BWAaln, BWAmem and SOAP3-?dp in 88.00, 48.68 and 46.27 hours, respectively.

They claimed that this performance gain did not come at the cost of quality.

BALSA (and SOAP3-?dp) has the highest alignment sensitivity. When measuring the number of read pairs that have both ends aligned and paired, SOAP3-?dp/BALSA reports 97.08%, BWAmem 95.74%, BWAaln 92.22% and ISAAC 91.42% (see table S1 for details).