{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T11:19:57Z","timestamp":1768475997971,"version":"3.49.0"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2019,1,12]],"date-time":"2019-01-12T00:00:00Z","timestamp":1547251200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000289","name":"Cancer Research UK","doi-asserted-by":"publisher","award":["20412"],"award-info":[{"award-number":["20412"]}],"id":[{"id":"10.13039\/501100000289","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000289","name":"Cancer Research UK","doi-asserted-by":"publisher","award":["22398"],"award-info":[{"award-number":["22398"]}],"id":[{"id":"10.13039\/501100000289","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>CRISPR\/Cas9 system requires short guide RNAs (sgRNAs) to direct genome modification. Most currently available tools for sgRNA design operate only with standard reference genomes, and are best suited for small-scale projects. To address these limitations, we developed Crisflash, a software tool for fast sgRNA design and potential off-target discovery, built for performance and flexibility. Crisflash can rapidly design CRISPR guides against any sequenced genome or genome sequences, and can optimize guide accuracy by incorporating user-supplied variant data. Crisflash is over an order of magnitude faster than comparable tools, even using a single CPU core, and efficiently and robustly scores the potential off-targeting of all possible candidate CRISPR guide oligonucleotides.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/crisflash<\/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\/btz019","type":"journal-article","created":{"date-parts":[[2019,1,8]],"date-time":"2019-01-08T15:41:10Z","timestamp":1546962070000},"page":"3146-3147","source":"Crossref","is-referenced-by-count":45,"title":["Crisflash: open-source software to generate CRISPR guide RNAs against genomes annotated with individual variation"],"prefix":"10.1093","volume":"35","author":[{"given":"Adrien L S","family":"Jacquin","sequence":"first","affiliation":[{"name":"Cancer Research UK Cambridge Institute, University of Cambridge , Cambridge, UK and"},{"name":"Cetrale Nantes , 44321 Nantes, Cedex 3, France"}]},{"given":"Duncan T","family":"Odom","sequence":"additional","affiliation":[{"name":"Cancer Research UK Cambridge Institute, University of Cambridge , Cambridge, UK and"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0701-5358","authenticated-orcid":false,"given":"Margus","family":"Lukk","sequence":"additional","affiliation":[{"name":"Cancer Research UK Cambridge Institute, University of Cambridge , Cambridge, UK and"}]}],"member":"286","published-online":{"date-parts":[[2019,1,12]]},"reference":[{"key":"2023062711304739800_btz019-B1","doi-asserted-by":"crossref","first-page":"1473","DOI":"10.1093\/bioinformatics\/btu048","article-title":"Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases","volume":"30","author":"Bae","year":"2014","journal-title":"Bioinformatics"},{"key":"2023062711304739800_btz019-B2","doi-asserted-by":"crossref","first-page":"e214.","DOI":"10.1038\/mtna.2014.64","article-title":"COSMID: a web-based tool for identifying and validating CRISPR\/Cas off-target sites","volume":"3","author":"Cradick","year":"2014","journal-title":"Mol. Ther. Nucleic Acids"},{"key":"2023062711304739800_btz019-B3","doi-asserted-by":"crossref","first-page":"822","DOI":"10.1038\/nbt.2623","article-title":"High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells","volume":"31","author":"Fu","year":"2013","journal-title":"Nat. Biotechnol"},{"key":"2023062711304739800_btz019-B4","doi-asserted-by":"crossref","first-page":"3078","DOI":"10.1093\/bioinformatics\/btv308","article-title":"WGE: a CRISPR database for genome engineering","volume":"31","author":"Hodgkins","year":"2015","journal-title":"Bioinformatics"},{"key":"2023062711304739800_btz019-B5","doi-asserted-by":"crossref","first-page":"827","DOI":"10.1038\/nbt.2647","article-title":"DNA targeting specificity of RNA-guided Cas9 nucleases","volume":"31","author":"Hsu","year":"2013","journal-title":"Nat. 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Protoc"},{"key":"2023062711304739800_btz019-B9","doi-asserted-by":"crossref","first-page":"e118","DOI":"10.1093\/nar\/gkv575","article-title":"Cas9-chromatin binding information enables more accurate CRISPR off-target prediction","volume":"43","author":"Singh","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023062711304739800_btz019-B10","doi-asserted-by":"crossref","first-page":"1180","DOI":"10.1093\/bioinformatics\/btt764","article-title":"CasOT: a genome-wide Cas9\/gRNA off-target searching tool","volume":"30","author":"Xiao","year":"2014","journal-title":"Bioinformatics"},{"key":"2023062711304739800_btz019-B11","doi-asserted-by":"crossref","first-page":"e108424.","DOI":"10.1371\/journal.pone.0108424","article-title":"CRISPRseek: a bioconductor package to identify target specific guide RNAs for CRISPR-Cas9 genome-editing systems","volume":"9","author":"Zhu","year":"2014","journal-title":"PLoS One"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/17\/3146\/50719757\/bioinformatics_35_17_3146.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/17\/3146\/50719757\/bioinformatics_35_17_3146.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,27]],"date-time":"2023-06-27T11:30:59Z","timestamp":1687865459000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/17\/3146\/5288510"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,1,12]]},"references-count":11,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2019,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz019","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,9,1]]},"published":{"date-parts":[[2019,1,12]]}}}