(GENE-IS_1.0)
Please cite the research article, if you use GENE-IS: Saira Afzal et al., 2016. GENE-IS: time-efficient and accurate analysis of viral integration events in large-scale gene therapy data. Molecular Therapy - Nucleic Acids 2016, vol. 6:133-139. DOI:https://doi.org/10.1016/j.omtn.2016.12.001
GENE-IS is a pipeline for the extraction of integration sites from next-generation sequencing data of clinical and preclinical gene therapy studies. It is specifically designed in order to accept the sequencing reads originated from different protocols like LAM (linear amplification mediated) PCR and Targeted Sequencing (SureSelect/AGILENT) methods.
The easiest way to obtain and run gene-is is cloning the present repository
mkdir path_to_location
cd path_to_location
git clone https://github.com/G100DKFZ/gene-is.git
cd gene-isTo test that the installation was successful we prepared testGenis.sh, a simple
script that run a fast analysis on a set of reduced datasets.
Type the following command on terminal for changing directory to scripts
cd /path_to_location/gene-is/scripts
# export the location of gene-is
export GENIS=/path_to_location/gene-is
# Run test suite by following command
./testGenis.shOn the terminal will appear these options;
1) Targeted Sequencing Pair BWA 4) All
2) Targeted Sequencing Single 5) Clear
3) LAM-PCR 6) QuitTo run tests for targeted sequencing paired end mode type at terminal 1 and press enter. If installation was successful following message will appear on the terminal "Targeted Sequencing Pair worked as expected!"
To run tests for targeted sequencing single end mode type at terminal 2 and press enter. If installation was successful following message will appear on the terminal "Targeted Sequencing Single end worked as expected!"
To run tests for LAM-PCR paired end mode type at terminal 3 and press enter. If installation was successful following message will appear on the terminal "LAM-PCR Pair worked as expected!"
In order to test the datasets used in the Manuscript for GENE-IS benchmarking, please see "README" file in "/path_to_location/gene-is/testFiles" directory
GENE-IS depends on several third party tools which are open source and are freely available.
All these tools are already provided within the GENE-IS package in $GENIS/tools/bin directory.
This folder is referred as default location for third party tools in the configuration files
#############################################################################
## Third-party tools
#Provide path to these third-party tools
#############################################################################
#Provide path to the BWA aligner
aligner = $GENIS/tools/bin/bwa
#Path to the secondary aligner. (BLAT)
blatAligner = $GENIS/tools/bin/blat
#Path to the trimming and filtering tool (Skewer)
skewer = $GENIS/tools/bin/skewer
#Path to the Samtools
samtools= $GENIS/tools/bin/samtools
#Path to the bedtools
bedTools= $GENIS/tools/bin/bedtoolsFor user information names of tools and related links are provided here; Tool Version URL
BWA 0.7.4 http://sourceforge.net/projects/bio-bwa/files/?source=navbar
Bedtools 2.17.0 https://code.google.com/p/bedtools/downloads/detail?name=BEDTools.v2.17.0.tar.gz&can=2&q=
Samtools 0.1.19 http://samtools.sourceforge.net/
BLAT v.35 http://users.soe.ucsc.edu/~kent/src/blatSrc35.zip
Skewer 0.1.117 http://sourceforge.net/projects/skewer/files/Binaries/
The required Perl libraries are pre-packaged within the tool ("lib" dir in GENE-IS).
GENE-IS has specific configuration files for each mode of analysis; LAM-PCR, TES paired and TES single end configuration files. 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.
$GENIS/configFile_targetedSequencing_pairedEnd.txt