MutantHuntWGS: A Pipeline for Identifying Saccharomyces cerevisiae Mutations
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 out...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Oxford University Press
2020-09-01
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| Series: | G3: Genes, Genomes, Genetics |
| Subjects: | |
| Online Access: | http://g3journal.org/lookup/doi/10.1534/g3.120.401396 |
| _version_ | 1818881805016629248 |
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| author | Mitchell A. Ellison Jennifer L. Walker Patrick J. Ropp Jacob D. Durrant Karen M. Arndt |
| author_facet | Mitchell A. Ellison Jennifer L. Walker Patrick J. Ropp Jacob D. Durrant Karen M. Arndt |
| author_sort | Mitchell A. Ellison |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-19T15:07:42Z |
| format | Article |
| id | doaj.art-9d292c92fce84fb99f49828aad98f29a |
| institution | Directory Open Access Journal |
| issn | 2160-1836 |
| language | English |
| last_indexed | 2024-12-19T15:07:42Z |
| publishDate | 2020-09-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | G3: Genes, Genomes, Genetics |
| spelling | doaj.art-9d292c92fce84fb99f49828aad98f29a2022-12-21T20:16:24ZengOxford University PressG3: Genes, Genomes, Genetics2160-18362020-09-011093009301410.1534/g3.120.40139611MutantHuntWGS: A Pipeline for Identifying Saccharomyces cerevisiae MutationsMitchell A. EllisonJennifer L. WalkerPatrick J. RoppJacob D. DurrantKaren M. ArndtMutantHuntWGS 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.http://g3journal.org/lookup/doi/10.1534/g3.120.401396mutant huntvariant callingsaccharomyces cerevisiaebulk segregant analysislab evolution |
| spellingShingle | Mitchell A. Ellison Jennifer L. Walker Patrick J. Ropp Jacob D. Durrant Karen M. Arndt MutantHuntWGS: A Pipeline for Identifying Saccharomyces cerevisiae Mutations G3: Genes, Genomes, Genetics mutant hunt variant calling saccharomyces cerevisiae bulk segregant analysis lab evolution |
| title | MutantHuntWGS: A Pipeline for Identifying Saccharomyces cerevisiae Mutations |
| title_full | MutantHuntWGS: A Pipeline for Identifying Saccharomyces cerevisiae Mutations |
| title_fullStr | MutantHuntWGS: A Pipeline for Identifying Saccharomyces cerevisiae Mutations |
| title_full_unstemmed | MutantHuntWGS: A Pipeline for Identifying Saccharomyces cerevisiae Mutations |
| title_short | MutantHuntWGS: A Pipeline for Identifying Saccharomyces cerevisiae Mutations |
| title_sort | mutanthuntwgs a pipeline for identifying saccharomyces cerevisiae mutations |
| topic | mutant hunt variant calling saccharomyces cerevisiae bulk segregant analysis lab evolution |
| url | http://g3journal.org/lookup/doi/10.1534/g3.120.401396 |
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