kelsi-kw/vseq-toolkit

README

(VSeq-Toolkit 1.1)

Please cite the research article, if you use VSeq-Toolkit: Saira Afzal et al., 2020. VSeq-Toolkit: Comprehensive Computational Analysis of Viral Vectors in Gene Therapy. Molecular Therapy - Methods & Clinical Development, Volume 17, 752 - 757. DOI; https://doi.org/10.1016/j.omtm.2020.03.024

VSeq-Toolkit is designed to analyze viral vector gene therapy sequencing data TES/WGS.

It has three modes Mode1;Contaminant Analysis, Mode2;Vector-Vector Fusion, Mode3;Vector-Host Fusion.

It is programmed in BASH and PERL.

Setup of VSeq-Toolkit

Installation procedure

Clone the repository from Github

git clone https://github.com/CompMeth/VSeq-Toolkit.git
cd VSeq-Toolkit

Testing

To test if the installation of VSeq-Toolkit was successfull

First export the location of VSeq-toolkit
export VSeqToolkit=/complete-path/VSeq-Toolkit

Second run the test suite by executing following two commands on terminal
Execute the program within output directory
mkdir $VSeqToolkit/testDir/testResultsCheck
cd $VSeqToolkit/testDir/testResultsCheck
perl $VSeqToolkit/scripts/VSeq-TK.pl -c $VSeqToolkit/config.test.txt
OR
perl -I $VSeqToolkit/scripts/ $VSeqToolkit/scripts/VSeq-TK.pl -c $VSeqToolkit/config.test.txt

If process runs without error then installation is successfull 
The final result files in this $VSeqToolkit/testDir/testResults directory should be same as result files in $VSeqToolkit/testDir/testResultsCheck

Dependencies

Third-party tools

VSeq-Toolkit requires third-party tools that are already packaged within toolkit's 'thirdPartyTools' directory. Tools (BWA-0.7.4, Skewer-0.1.117, Sametools-1.3.1, Bedtools-2.17.0) The required Perl library is within the scripts directory.

$VSeqToolkit/thirdPartyTools

Configuration file

The config.txt file can be used to analyze all three modes independently OR Mode1, Mode2 and Mode3 Only the relevant configuration file should be modified for particular analysis. For testing GENE-IS installation user does not need to change any parameter in the configuration file. The templates are in the gene-is path; i.e.

$VSeqToolkit/config.txt

VSeq-Toolkit only for research purpose

• Contact: [email protected], [email protected]