(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.
Clone the repository from Github
git clone https://github.com/CompMeth/VSeq-Toolkit.git
cd VSeq-Toolkit
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
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
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]