Crisflash: Open-source software to generate CRISPR guide RNAs against genomes annotated with individual variation
Open accessAbstract
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.
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Crisflash is a tool for both sgRNA design and latent off-target discovery, and it is over an order of magnitude faster than other software.
“Crisflash is a tool for both sgRNA design and latent off-target discovery, which is over an order of magnitude faster than other software (Jacquin et al., 2019).”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as Jacquin et al., 2019
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Cites
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“Crisflash is a tool for both sgRNA design and latent off-target discovery, which is over an order of magnitude faster than other software (Jacquin et al., 2019).”
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“Crisflash utilises a tree-based algorithm to rapidly design CRISPR guide RNAs and optimise guide accuracy by incorporating user-supplied variant data [43].”
BackgroundMethodTools for experimental and computational analyses of off-target editing by programmable nucleases
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“…BWA as search engine, methods like GuideScan (Perez et al., 2017), Cas-OFFinder (Bae et al., 2014), FlashFry (McKenna and Shendure, 2018), Cris fl ash (Jacquin et al., 2019), CRISPRitz (Cancellieri et al., 2020), and fi nally, CRISPR-SE (Li et al., 2021)are faster due to the use of Brute force…”
BackgroundMethodInfluentialBest practice for CRISPR design using current tools and resources
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“Current tools such as Crisflash (54) and CRISPR-Local (84) considering only somatic mutation are far from satisfactory.”
BackgroundMethodLiu, Z., Liu, J., Yang, Z., Zhū, L., Zhu, Z., Huang, H., & Jiang, L. (2023) · Biotechnology Advances · doi:10.1016/j.biotechadv.2023.108241 · Cited by 16 · see citing works
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“%) hg38 mm10 hg38 mm10 hg38 mm10 hg38 mm10 (A) Accuracy comparisons: Alignment tools: BLAST 99 99 46 43 26 31 7 8 BLAT 88 94 51 50 48 57 36 39 Bowtie 100 100 100 100 100 100 0 0 Bowtie2 100 100 24 15 0 0 0 0 BWA 25 36 0 0 0 0 0 0 Brute force: CRISPR-SE 100 100 100 100 100 100 100 100 (B) Speed comparisons: 1-mm(s) 2-m…”
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“TVIR 2.0 uses Crisflash (https://github.com/ /crisflash/) software to design gRNAs,which can rapidly design gRNAs against any genome sequences,and can optimize guide accuracy by incorporating user-supplied variant data [46].”
InfluentialCRISPR technology in human diseases
Feng, Q., Li, Q., Zhou, H., Wang, Z., Lin, C., Jiang, Z., Liu, T., & Wang, D. (2024) · MedComm · doi:10.1002/mco2.672 · Cited by 7 · see citing works
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- Authors
- Jacquin, A. L. S., Odom, D. T., & Lukk, M.
- Affiliations
- University of Cambridge (GB)
- Corresponding author
- Lukk, Margus
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2019-01-12
- Volume
- 35
- Issue
- 17
- Pages
- 3146-3147
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC6735888
- OpenAlex
- W2909458562
- Cited by
- 46
- References
- 11
- Citations by year
- 2026: 2 · 2025: 5 · 2024: 13 · 2023: 5 · 2022: 7 · 2021: 4 · 2020: 7 · 2019: 3
- FWCI
- 1.74
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Bioinformatics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Apollo (University of Cambridge) (submittedVersion, cc-by)
- Apollo (cc-by)
- Funders
- Cancer Research UK (20412, 22398)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- CRISPR/Cas9, guide RNA design, sgRNA design, off-target prediction, genome modification, open source software
- MeSH terms
- Gene Editing, RNA, Guide, CRISPR-Cas Systems, Base Sequence, Software, Genome, RNA, Guide, Kinetoplastida, Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR-Cas Systems
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