{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T01:38:36Z","timestamp":1773797916480,"version":"3.50.1"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2020,8,11]],"date-time":"2020-08-11T00:00:00Z","timestamp":1597104000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Deutsche Forschungsgemeinschaft (DFG, German Research Foundation","award":["39068611"],"award-info":[{"award-number":["39068611"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Mutation-Simulator allows the introduction of various types of sequence alterations in reference sequences, with reasonable compute-time even for large eukaryotic genomes. Its intuitive system for fine-grained control over mutation rates along the sequence enables the mimicking of natural mutation patterns. Using standard file formats for input and output data, it can easily be integrated into any development and benchmarking workflow for high-throughput sequencing applications.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Mutation-Simulator is written in Python 3 and the source code, documentation, help and use cases are available on the Github page at https:\/\/github.com\/mkpython3\/Mutation-Simulator. It is free for use under the GPL 3 license.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa716","type":"journal-article","created":{"date-parts":[[2020,8,5]],"date-time":"2020-08-05T19:31:54Z","timestamp":1596655914000},"page":"568-569","source":"Crossref","is-referenced-by-count":41,"title":["Mutation-Simulator: fine-grained simulation of random mutations in any genome"],"prefix":"10.1093","volume":"37","author":[{"given":"M A","family":"K\u00fchl","sequence":"first","affiliation":[{"name":"Quantitative Genetics and Genomics of Plants, Heinrich Heine University , D\u00fcsseldorf 40225, Germany"}]},{"given":"B","family":"Stich","sequence":"additional","affiliation":[{"name":"Quantitative Genetics and Genomics of Plants, Heinrich Heine University , D\u00fcsseldorf 40225, Germany"}]},{"given":"D C","family":"Ries","sequence":"additional","affiliation":[{"name":"Quantitative Genetics and Genomics of Plants, Heinrich Heine University , D\u00fcsseldorf 40225, Germany"}]}],"member":"286","published-online":{"date-parts":[[2020,8,11]]},"reference":[{"key":"2023051706065836700_btaa716-B1","doi-asserted-by":"crossref","first-page":"428","DOI":"10.1186\/s12859-017-1831-5","article-title":"SimBA: a methodology and tools for evaluating the performance of RNA-Seq bioinformatic pipelines","volume":"18","author":"Audoux","year":"2017","journal-title":"BMC Bioinformatics"},{"key":"2023051706065836700_btaa716-B2","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1038\/nrg.2016.57","article-title":"A comparison of tools for the simulation of genomic next-generation sequencing data","volume":"17","author":"Escalona","year":"2016","journal-title":"Nat. Rev. Genet"},{"key":"2023051706065836700_btaa716-B3","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-019-09406-4","article-title":"Systematic benchmarking of omics computational tools","volume":"10","author":"Mangul","year":"2019","journal-title":"Nat. Commun"},{"key":"2023051706065836700_btaa716-B4","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1126\/science.1180677","article-title":"The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana","volume":"327","author":"Ossowski","year":"2010","journal-title":"Science"},{"key":"2023051706065836700_btaa716-B5","doi-asserted-by":"crossref","first-page":"1876","DOI":"10.1093\/bioinformatics\/btx091","article-title":"Simulome: a genome sequence and variant simulator","volume":"33","author":"Price","year":"2017","journal-title":"Bioinformatics"},{"key":"2023051706065836700_btaa716-B6","doi-asserted-by":"crossref","first-page":"4442","DOI":"10.1093\/bioinformatics\/btz424","article-title":"simuG: a general-purpose genome simulator","volume":"35","author":"Yue","year":"2019","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa716\/34036760\/btaa716.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/4\/568\/50359780\/btaa716.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/4\/568\/50359780\/btaa716.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,17]],"date-time":"2023-05-17T06:12:01Z","timestamp":1684303921000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/37\/4\/568\/5891169"}},"subtitle":[],"editor":[{"given":"Inanc","family":"Birol","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,8,11]]},"references-count":6,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2021,5,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa716","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,2,15]]},"published":{"date-parts":[[2020,8,11]]}}}