exgen's Introduction

ExGen[Archived]

ExGen is a bpipe and Perl based whole Exome and Genome analysis pipeline. The pipeline was designed primarily to take advantage of a multi-node HPC environment though it also supports single node environments. The pipeline can be used for

Major features of the pipeline are:-

Easy single command launch for any number of input samples
Customizable mail notifications on completion of pipeline/ individual stages
Monitoring of the run with sample and stage wise status
Out of the box support for running on HPC environment with multiple job managers eg. lsf, torque etc supported
Inbuilt validation of tools, parameters and input files
Customizable tool flow and easy resume from any intermediate step in case of failure
Integrated collection of relevant statistics from every stage and collation into a single excel file for easy comprison and summarization
All fastqc images are collected into a single directory for easy comparison of pre and post QC
Analysis of time taken per module/tool
Logging of all the executed commands for easy traceback of parameters

Limitations:-

Currently supports only paired end Illumina data out of the box. Though pipeline can be easily edited to single end mode, different toolbase etc.

TODO:-

Reduction of consumed disk space with compression of BAM files using CRAM or alternate toolkit
Relevant plots for the collected statistics
Creation of a dockerised container with all the dependencies
Add test cases for multi node/single node use case scenarios

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