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 CRISPR guideRNA design and analysis

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A more flexible version of Guidescan2 is offered as a command line interface at: github.com/schmidt73/guidescan-cli. Common use cases and complete documentation is well-described in the attached manual. For ease of use we make available a set of pre-constructed indices for several genomes that can be used with the command line version of our software for a variety of tasks. In addition, we provide the raw Guidescan2 databases produced by our tool for several organism-enzyme combinations in a compressed BAM format. The exact details of the format are described in the software manual.

The indices can be browsed at /indices and /databases. We also put them in the following tables for your convenience.

Guidescan2 Indices:


#OrganismShorthandRefSeq AccessionDownload
1Fruit Flydm6GCF_000001215.4dm6
2Humanhg38GCF_000001405.39hg38
3House Mousemm10GCF_000001635.26mm10
4House Mousemm39GCF_000001635.27mm39
5Baker's YeastsacCer3GCF_000146045.2sacCer3
6Norway Ratrn6GCF_015227675.2rn6
7Nematodece11GCF_000002985.6ce11

Guidescan2 Databases:


#OrganismShorthandEnzymeRefSeq AccessionDownload
1Fruit Flydm6cas9GCF_000001215.4dm6
2Humanhg38cpf1GCF_000001405.39hg38
3Humanhg38cas9GCF_000001405.39hg38
4Humanhg38_no_altcas9GCF_000001405.26hg38_no_alt
5Humant2t_chm13cas9GCF_009914755.1t2t_chm13
6House Mousemm10cpf1GCF_000001635.26mm10
7House Mousemm10cas9GCF_000001635.26mm10
8House Mousemm10_no_altcas9GCF_000001635.26mm10_no_alt
9House Mousemm39cas9GCF_000001635.27mm39
10Baker's YeastsacCer3cas9GCF_000146045.2sacCer3
11Norway Ratrn6cas9GCF_015227675.2rn6
12Nematodece11cpf1GCF_000002985.6ce11
13Nematodece11cas9GCF_000002985.6ce11