The In Silico Genotyper (ISG): an open-source pipeline to rapidly identify and annotate nucleotide variants for comparative genomics applications

Abstract

The identification and annotation of nucleotide variants, including insertions/deletions and single nucleotide polymorphisms (SNPs), from whole genome sequence data is important for studies of bacterial evolution, comparative genomics, and phylogeography. The in silico Genotyper (ISG) represents a parallel, tested, open source tool that can perform these functions and scales well to thousands of bacterial genomes. ISG is written in Java and requires MUMmer (Delcher, et al., 2003), BWA (Li and Durbin, 2009), and GATK (McKenna, et al., 2010) for full functionality. The source code and compiled binaries are freely available from https://github.com/TGenNorth/ISGPipeline under a GNU General Public License. Benchmark comparisons demonstrate that ISG is faster and more flexible than comparable tools.