ISVDA

Iterative Small Variant Discovery Algorithm

Prerequisites

• Python 2.7
• g++
• SAMtools
• BWA/Bowtie2 (ISVDA supports BWA and Bowtie2, according to our experiment, BWA runs faster, so the default support is BWA, you can use -e to indicate using Bowtie2)
• Freebayes (To use multi-thread mode of ISVDA, parallel version of Freebayes must be downloaded from: https://github.com/ekg/freebayes/blob/master/scripts/freebayes-parallel, and using --parallel_freebayes to indicate the directory)

Installation

1. Download repositories
2. cd isvda
3. make

Usage:

Multithreading Mode Quick Usage : (This requires samtools and bwa in PATH, i.e. you can directly run samtools and bwa. This also need freebayes-parallel directory indicated correctly.)

python isvda.py -r whole_genome.fa -p 1.fastq 2.fastq -i 6 -w workspace_directory -t 8 -g --parallel_freebayes=parallel_freebayes_directory

Detail Usage:

python isvda.py -h