Crisflash: open-source software to generate CRISPR guide RNAs against genomes annotated with individual variation.

Szczegóły
Abstrakt

Tytuł:: Crisflash: open-source software to generate CRISPR guide RNAs against genomes annotated with individual variation.
Autorzy:: Jacquin ALS; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK and.; Cetrale Nantes, 44321 Nantes, Cedex 3, France.
Odom DT; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK and.
Lukk M; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK and.
Źródło:: Bioinformatics (Oxford, England) [Bioinformatics] 2019 Sep 01; Vol. 35 (17), pp. 3146-3147.
Typ publikacji:: Journal Article; Research Support, Non-U.S. Gov't
Język:: English
Imprint Name(s):: Original Publication: Oxford : Oxford University Press, c1998-
MeSH Terms:: Clustered Regularly Interspaced Short Palindromic Repeats*
Genome*
Base Sequence ; CRISPR-Cas Systems ; Gene Editing ; RNA, Guide, CRISPR-Cas Systems ; Software
References:: Nat Biotechnol. 2013 Sep;31(9):822-6. (PMID: 23792628)
Nat Biotechnol. 2013 Sep;31(9):827-32. (PMID: 23873081)
Nat Protoc. 2013 Nov;8(11):2281-2308. (PMID: 24157548)
Bioinformatics. 2014 Apr 15;30(8):1180-1182. (PMID: 24389662)
Bioinformatics. 2014 May 15;30(10):1473-5. (PMID: 24463181)
PLoS One. 2014 Sep 23;9(9):e108424. (PMID: 25247697)
Bioinformatics. 2015 Apr 1;31(7):1120-3. (PMID: 25414360)
Mol Ther Nucleic Acids. 2014 Dec 02;3:e214. (PMID: 25462530)
Bioinformatics. 2015 Sep 15;31(18):3078-80. (PMID: 25979474)
Nucleic Acids Res. 2015 Oct 15;43(18):e118. (PMID: 26032770)
Nucleic Acids Res. 2016 Jul 8;44(W1):W272-6. (PMID: 27185894)
Grant Information:: 202878/Z/16/Z United Kingdom WT_ Wellcome Trust; 22398 United Kingdom CRUK_ Cancer Research UK; 20412 United Kingdom CRUK_ Cancer Research UK
Substance Nomenclature:: 0 (RNA, Guide, CRISPR-Cas Systems)
Entry Date(s):: Date Created: 20190117 Date Completed: 20200617 Latest Revision: 20240104
Update Code:: 20240104
PubMed Central ID:: PMC6735888
DOI:: 10.1093/bioinformatics/btz019
PMID:: 30649181
: Czasopismo naukowe

Summary: 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.
Availability and Implementation: https://github.com/crisflash.
Supplementary Information: Supplementary data are available at Bioinformatics online.
(© The Author(s) 2019. Published by Oxford University Press.)

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