QPL-enabled HTSlib library: accelerating sequence file compression using Intel IAA.

Abstract

Summary: Sequence analysis workflows require the accessibility of large datasets, which require state-of-the-art compression tools. These compression tools, such as Samtools, often rely on HTSlib as a GZip implementation, but are still limited by throughput on time-intensive compression. QPL-HTSLib offers order of magnitude speedups for the compression and decompression of the SAM and BAM file formats commonly used in genomics workflows at the cost of a slightly larger compressed file, and is a drop-in replacement for HTSlib on Intel systems.

Availability and implementation: QPL-HTSLib is freely available on Github as an open-source software project.