Whisper 2: 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 Whisper 2, 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.