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:
# | Organism | Shorthand | RefSeq Accession | Download |
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1 | Fruit Fly | dm6 | GCF_000001215.4 | dm6 |
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2 | Human | hg38 | GCF_000001405.39 | hg38 |
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3 | House Mouse | mm10 | GCF_000001635.26 | mm10 |
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4 | House Mouse | mm39 | GCF_000001635.27 | mm39 |
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5 | Baker's Yeast | sacCer3 | GCF_000146045.2 | sacCer3 |
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6 | Norway Rat | rn6 | GCF_015227675.2 | rn6 |
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7 | Nematode | ce11 | GCF_000002985.6 | ce11 |
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Guidescan2 Databases:
# | Organism | Shorthand | Enzyme | RefSeq Accession | Download |
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1 | Fruit Fly | dm6 | cas9 | GCF_000001215.4 | dm6 |
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2 | Human | hg38 | cpf1 | GCF_000001405.39 | hg38 |
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3 | Human | hg38 | cas9 | GCF_000001405.39 | hg38 |
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4 | Human | hg38_no_alt | cas9 | GCF_000001405.26 | hg38_no_alt |
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5 | Human | t2t_chm13 | cas9 | GCF_009914755.1 | t2t_chm13 |
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6 | House Mouse | mm10 | cpf1 | GCF_000001635.26 | mm10 |
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7 | House Mouse | mm10 | cas9 | GCF_000001635.26 | mm10 |
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8 | House Mouse | mm10_no_alt | cas9 | GCF_000001635.26 | mm10_no_alt |
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9 | House Mouse | mm39 | cas9 | GCF_000001635.27 | mm39 |
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10 | Baker's Yeast | sacCer3 | cas9 | GCF_000146045.2 | sacCer3 |
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11 | Norway Rat | rn6 | cas9 | GCF_015227675.2 | rn6 |
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12 | Nematode | ce11 | cpf1 | GCF_000002985.6 | ce11 |
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13 | Nematode | ce11 | cas9 | GCF_000002985.6 | ce11 |
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