MutantHuntWGS: A Pipeline for Identifying Saccharomyces cerevisiae Mutations

G3 (Bethesda). 2020 Sep 2;10(9):3009-3014. doi: 10.1534/g3.120.401396.


MutantHuntWGS is a user-friendly pipeline for analyzing Saccharomyces cerevisiae whole-genome sequencing data. It uses available open-source programs to: (1) perform sequence alignments for paired and single-end reads, (2) call variants, and (3) predict variant effect and severity. MutantHuntWGS outputs a shortlist of variants while also enabling access to all intermediate files. To demonstrate its utility, we use MutantHuntWGS to assess multiple published datasets; in all cases, it detects the same causal variants reported in the literature. To encourage broad adoption and promote reproducibility, we distribute a containerized version of the MutantHuntWGS pipeline that allows users to install and analyze data with only two commands. The MutantHuntWGS software and documentation can be downloaded free of charge from

Keywords: Mutant hunt; Saccharomyces cerevisiae; bulk segregant analysis; lab evolution; variant calling.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • High-Throughput Nucleotide Sequencing*
  • Mutation
  • Reproducibility of Results
  • Saccharomyces cerevisiae* / genetics
  • Software