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MuWU: Mutant-seq library analysis and annotation
MOTIVATION: Insertional mutagenesis allows for the creation of loss-of-function mutations on a genome-wide scale. In theory, every gene can be ‘knocked out’ via the insertion of an additional DNA sequence. Resources of sequence-indexed mutants of plant and animal model organisms are instrumental for...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8756183/ https://www.ncbi.nlm.nih.gov/pubmed/34586393 http://dx.doi.org/10.1093/bioinformatics/btab679 |
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author | Stöcker, Tyll Altrogge, Lena Marcon, Caroline Win, Yan Naing Hochholdinger, Frank Schoof, Heiko |
author_facet | Stöcker, Tyll Altrogge, Lena Marcon, Caroline Win, Yan Naing Hochholdinger, Frank Schoof, Heiko |
author_sort | Stöcker, Tyll |
collection | PubMed |
description | MOTIVATION: Insertional mutagenesis allows for the creation of loss-of-function mutations on a genome-wide scale. In theory, every gene can be ‘knocked out’ via the insertion of an additional DNA sequence. Resources of sequence-indexed mutants of plant and animal model organisms are instrumental for functional genomics studies. Such repositories significantly speed up the acquisition of interesting genotypes and allow for the validation of hypotheses regarding phenotypic consequences in reverse genetics. To create such resources, comprehensive sequencing of flanking sequence tags using protocols such as Mutant-seq requires various downstream computational tasks, and these need to be performed in an efficient and reproducible manner. RESULTS: Here, we present MuWU, an automated Mutant-seq workflow utility initially created for the identification of Mutator insertion sites of the BonnMu resource, representing a reverse genetics mutant collection for functional genetics in maize (Zea mays). MuWU functions as a fast, one-stop downstream processing pipeline of Mutant-seq reads. It takes care of all complex bioinformatic tasks, such as identifying tagged genes and differentiating between germinal and somatic mutations/insertions. Furthermore, MuWU automatically assigns insertions to the corresponding mutated seed stocks. We discuss the implementation and how parameters can easily be adapted to use MuWU for other species/transposable elements. AVAILABILITY AND IMPLEMENTATION: MuWU is a Snakemake-based workflow and freely available at https://github.com/tgstoecker/MuWU. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. |
format | Online Article Text |
id | pubmed-8756183 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-87561832022-01-13 MuWU: Mutant-seq library analysis and annotation Stöcker, Tyll Altrogge, Lena Marcon, Caroline Win, Yan Naing Hochholdinger, Frank Schoof, Heiko Bioinformatics Applications Notes MOTIVATION: Insertional mutagenesis allows for the creation of loss-of-function mutations on a genome-wide scale. In theory, every gene can be ‘knocked out’ via the insertion of an additional DNA sequence. Resources of sequence-indexed mutants of plant and animal model organisms are instrumental for functional genomics studies. Such repositories significantly speed up the acquisition of interesting genotypes and allow for the validation of hypotheses regarding phenotypic consequences in reverse genetics. To create such resources, comprehensive sequencing of flanking sequence tags using protocols such as Mutant-seq requires various downstream computational tasks, and these need to be performed in an efficient and reproducible manner. RESULTS: Here, we present MuWU, an automated Mutant-seq workflow utility initially created for the identification of Mutator insertion sites of the BonnMu resource, representing a reverse genetics mutant collection for functional genetics in maize (Zea mays). MuWU functions as a fast, one-stop downstream processing pipeline of Mutant-seq reads. It takes care of all complex bioinformatic tasks, such as identifying tagged genes and differentiating between germinal and somatic mutations/insertions. Furthermore, MuWU automatically assigns insertions to the corresponding mutated seed stocks. We discuss the implementation and how parameters can easily be adapted to use MuWU for other species/transposable elements. AVAILABILITY AND IMPLEMENTATION: MuWU is a Snakemake-based workflow and freely available at https://github.com/tgstoecker/MuWU. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2021-09-29 /pmc/articles/PMC8756183/ /pubmed/34586393 http://dx.doi.org/10.1093/bioinformatics/btab679 Text en © The Author(s) 2021. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Applications Notes Stöcker, Tyll Altrogge, Lena Marcon, Caroline Win, Yan Naing Hochholdinger, Frank Schoof, Heiko MuWU: Mutant-seq library analysis and annotation |
title | MuWU: Mutant-seq library analysis and annotation |
title_full | MuWU: Mutant-seq library analysis and annotation |
title_fullStr | MuWU: Mutant-seq library analysis and annotation |
title_full_unstemmed | MuWU: Mutant-seq library analysis and annotation |
title_short | MuWU: Mutant-seq library analysis and annotation |
title_sort | muwu: mutant-seq library analysis and annotation |
topic | Applications Notes |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8756183/ https://www.ncbi.nlm.nih.gov/pubmed/34586393 http://dx.doi.org/10.1093/bioinformatics/btab679 |
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