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MutantHuntWGS: A Pipeline for Identifying Saccharomyces cerevisiae Mutations.

ABSTRACT: 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 https://github.com/mae92/MutantHuntWGS.

SUBMITTER: Ellison MA

PROVIDER: S-EPMC7466961 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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MutantHuntWGS: A Pipeline for Identifying <i>Saccharomyces cerevisiae</i> Mutations.

Ellison Mitchell A MA Walker Jennifer L JL Ropp Patrick J PJ Durrant Jacob D JD Arndt Karen M KM

G3 (Bethesda, Md.) 20200902 9

MutantHuntWGS is a user-friendly pipeline for analyzing <i>Saccharomyces cerevisiae</i> 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 detec ...[more]

PMID: 32605926

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