MultiGuideScan

A multi-processing tool for designing CRISPR guide RNA library. MultiGuideScan parallelizes the workflow of GuideScan (https://bitbucket.org/arp2012/guidescan_public) with the multi-processing mechanism and uses the preprocessing optimization method to improve the computational efficiency.

Ensure the following dependencies are present

:::system
    samtools 1.3.1
    easy_install
    coreutils (shuf)
    rename
    python 2.7
    biopython>=1.66
    pysam==0.8.3
    pyfaidx==0.4.7.1
    bx-python==0.7.3
    
    for Rule Set 2 on-target cutting efficiency scores (this must be installed by user: https://pypi.python.org/pypi/scikit-learn/0.16.1)
    sklearn==0.16.1

To install, run

:::system
    python setup.py install

This will install binaries guidescan_processer, guidescan_bamdata, guidescan_guidequery, guidescan_cutting_efficiency_processer, guidescan_cutting_efficiency_processer.

After installation, use

:::python
    from guidescan import *

in your python session to import all modules of the package, or use

:::python
    from guidescan import guidequery

to import a particular module and then use functions from the module

:::python
    guidequery.query_bam()

For local installation, run something like

:::system
    python setup.py install --user

and then make sure that the local directory with binaries (such as $HOME/Library/Python/2.7/bin/) is available in your PATH.

For more info on full pipeline of guideRNA database construction from genomic sequences run

:::system
    guidescan_processer -h

For more info on guideRNA database construction with custom parameters using previously computed trie run

:::system
    guidescan_bamdata -h

For more info on accessing precomputed guideRNA database run

:::system
    guidescan_guidequery -h

For more info on computing cutting efficiency scores for Cas9 20mer gRNAs

:::system
	guidescan_cutting_efficiency_processer -h

For more info on computing cutting specificity scores for Cas9 20mer gRNAs

:::system
	guidescan_cutting_specificity_processer -h

bioinfomaticsCSU/MultiGuideScan

MultiGuideScan