{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,3]],"date-time":"2025-09-03T10:22:37Z","timestamp":1756894957936,"version":"3.37.3"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2021,9,29]],"date-time":"2021-09-29T00:00:00Z","timestamp":1632873600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/2.zoppoz.workers.dev:443\/https\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["MA 8427\/1-1"],"award-info":[{"award-number":["MA 8427\/1-1"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Insertional mutagenesis allows for the creation of loss-of-function mutations on a genome-wide scale. In theory, every gene can be \u2018knocked out\u2019 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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>MuWU is a Snakemake-based workflow and freely available at https:\/\/2.zoppoz.workers.dev:443\/https\/github.com\/tgstoecker\/MuWU.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab679","type":"journal-article","created":{"date-parts":[[2021,9,23]],"date-time":"2021-09-23T21:42:43Z","timestamp":1632433363000},"page":"837-838","source":"Crossref","is-referenced-by-count":4,"title":["MuWU: Mutant-seq library analysis and annotation"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/2.zoppoz.workers.dev:443\/https\/orcid.org\/0000-0001-7184-9472","authenticated-orcid":false,"given":"Tyll","family":"St\u00f6cker","sequence":"first","affiliation":[{"name":"Crop Bioinformatics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn , 53115 Bonn, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/2.zoppoz.workers.dev:443\/https\/orcid.org\/0000-0002-6871-235X","authenticated-orcid":false,"given":"Lena","family":"Altrogge","sequence":"additional","affiliation":[{"name":"Crop Bioinformatics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn , 53115 Bonn, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/2.zoppoz.workers.dev:443\/https\/orcid.org\/0000-0001-6699-9441","authenticated-orcid":false,"given":"Caroline","family":"Marcon","sequence":"additional","affiliation":[{"name":"Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn , 53115 Bonn, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/2.zoppoz.workers.dev:443\/https\/orcid.org\/0000-0002-4043-5194","authenticated-orcid":false,"given":"Yan Naing","family":"Win","sequence":"additional","affiliation":[{"name":"Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn , 53115 Bonn, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/2.zoppoz.workers.dev:443\/https\/orcid.org\/0000-0002-5155-0884","authenticated-orcid":false,"given":"Frank","family":"Hochholdinger","sequence":"additional","affiliation":[{"name":"Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn , 53115 Bonn, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/2.zoppoz.workers.dev:443\/https\/orcid.org\/0000-0002-1527-3752","authenticated-orcid":false,"given":"Heiko","family":"Schoof","sequence":"additional","affiliation":[{"name":"Crop Bioinformatics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn , 53115 Bonn, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,9,29]]},"reference":[{"key":"2023020108480621600_btab679-B1","doi-asserted-by":"crossref","first-page":"653","DOI":"10.1126\/science.1086391","article-title":"Genome-wide insertional mutagenesis of Arabidopsis thaliana","volume":"301","author":"Alonso","year":"2003","journal-title":"Science"},{"key":"2023020108480621600_btab679-B2","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1023\/B:PLAN.0000036368.74758.66","article-title":"Rice mutant resources for gene discovery","volume":"54","author":"Hirochika","year":"2004","journal-title":"Plant Mol. Biol"},{"key":"2023020108480621600_btab679-B3","doi-asserted-by":"crossref","first-page":"2520","DOI":"10.1093\/bioinformatics\/bts480","article-title":"Snakemake-a scalable bioinformatics workflow engine","volume":"28","author":"K\u00f6ster","year":"2012","journal-title":"Bioinformatics"},{"key":"2023020108480621600_btab679-B4","doi-asserted-by":"crossref","first-page":"1404","DOI":"10.1104\/pp.19.00894","article-title":"A sequence-indexed mutator insertional library for maize functional genomics study","volume":"181","author":"Liang","year":"2019","journal-title":"Plant Physiol"},{"key":"2023020108480621600_btab679-B5","doi-asserted-by":"crossref","first-page":"620","DOI":"10.1104\/pp.20.00478","article-title":"BonnMu: a sequence-indexed resource of transposon- induced maize mutations for functional genomics studies","volume":"184","author":"Marcon","year":"2020","journal-title":"Plant Physiol"},{"key":"2023020108480621600_btab679-B6","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1111\/j.1365-313X.2005.02509.x","article-title":"Steady-state transposon mutagenesis in inbred maize","volume":"44","author":"McCarty","year":"2005","journal-title":"Plant J"},{"key":"2023020108480621600_btab679-B7","doi-asserted-by":"crossref","first-page":"e77172","DOI":"10.1371\/journal.pone.0077172","article-title":"Mu-seq: sequence-based mapping and identification of transposon induced mutations","volume":"8","author":"McCarty","year":"2013","journal-title":"PLoS One"},{"key":"2023020108480621600_btab679-B8","doi-asserted-by":"crossref","first-page":"D1146","DOI":"10.1093\/nar\/gky1046","article-title":"Maizegdb 2018: the maize multi-genome genetics and genomics database","volume":"47","author":"Portwood","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2023020108480621600_btab679-B9","doi-asserted-by":"crossref","first-page":"731","DOI":"10.1111\/j.1365-313X.2011.04827.x","article-title":"\"Genome-wide LORE1 retrotransposon mutagenesis and high-throughput insertion detection in Lotus japonicus\"","volume":"69","author":"Urba\u0144ski","year":"2012","journal-title":"Plant J"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/2.zoppoz.workers.dev:443\/http\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btab679\/40533113\/btab679.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/2.zoppoz.workers.dev:443\/https\/academic.oup.com\/bioinformatics\/article-pdf\/38\/3\/837\/49007518\/btab679.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/2.zoppoz.workers.dev:443\/https\/academic.oup.com\/bioinformatics\/article-pdf\/38\/3\/837\/49007518\/btab679.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T20:05:56Z","timestamp":1675281956000},"score":1,"resource":{"primary":{"URL":"https:\/\/2.zoppoz.workers.dev:443\/https\/academic.oup.com\/bioinformatics\/article\/38\/3\/837\/6377773"}},"subtitle":[],"editor":[{"given":"Tobias","family":"Marschall","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2021,9,29]]},"references-count":9,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2022,1,12]]}},"URL":"https:\/\/2.zoppoz.workers.dev:443\/https\/doi.org\/10.1093\/bioinformatics\/btab679","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2022,2,1]]},"published":{"date-parts":[[2021,9,29]]}}}