Whisper2: Indel-sensitive short read mapping

Abstract

Identification of genetic variants is of crucial importance in the forthcoming era of precision medicine. Since the majority of variant callers require mapping reads to a reference genome, the reliability of the latter is a key factor determining accuracy of the downstream analyses. We present Whisper2, a short-read-mapping software providing superior quality of indel variant calling. Its running times place it among the fastest existing tools. The software is available at GitHub (https://github.com/refresh-bio/whisper) under GNU GPL 3 license.

Keywords

• Short read mapping
• High throughput sequencing
• Variant calling