crispor_cli

# CRISPOR - a CRISPR/Cas9 assistant

CRISPOR predicts off-targets in the genome, ranks guides, highlights problematic guides, designs primers and helps with cloning. Try it on

CRISPOR uses BWA, a few tools from the UCSC Genome Browser (twoBitToFa, bedClip), various R packages and a huge collection of external packages and source code files from published articles, see the file crisporEffScores.py for the exact references.

Installation of the package:

> make crispor_env > > source crispor_env/bin/activate > > make devbuild

Install required R libraries:

> sudo Rscript -e 'install.packages(c("e1071"), > repos="")' sudo Rscript -e > 'source(""); > biocLite(c("limma"));'

Now in a python console type this:

> from crispor_cli import crispor > > crispor.main(args,options)

Description for args and options is given below:
args=[<genome_name>,<input_fasta>,<output_file>]

Here args is a list containing org,fastaInFile and guideOutFile in this order:
Example args - args=['sacCer3','/input/guide_yeast.fasta','/output/yo_guide.tsv']

And options is a dictionary containing all the extra options permitted by crispor.
Example options -
options = {'offtargetFname':'/output/yo_off.tsv','pam':'NGG','debug':True,'skipAlign':True}

Here are the keys that can be added to options dictionary-

Options:
debug - show debug messages, do not delete temp directory test - run internal tests pam - PAM-motif to use, default NGG. TTTN triggers special Cpf1 behavior: no scores anymore + the PAM is assumed to be 5' of the guide. Common PAMs are: NGG,TTTN,NGA,NGCG,NNAGAA,NGGNG,NNGRRT,NNNNGMTT,NNNNACA offtargetFname - write offtarget info to this filename maxOcc - MAXOCC parameter, guides with more matches are excluded

mismatches- maximum number of mismatches, default 4

skipAlign - do not align the input sequence. The on-target will be
a random match with 0 mismatches.

noEffScores - do not calculate the efficiency scores minAltPamScore - minimum MIT off-target score for alternative PAMs, default 1.0 genomeDir- directory with genomes, default ./genomes

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# Licenses

Included software:

• BWA is under GPL3

• libSVM: under copyright by Chih-Chung Chang and Chih-Jen Lin see

• svmlight: free for non-commercial use, see

• SSC: no license specified

• primer3: GPL2.

• Fusi/Doench score: see LICENSE.txt, (c) by Microsoft Research

• crispor.py and crisporEffScores.py themselves are released under GPLv3, see LICENSE.txt