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

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 S ilico 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][1]), BWA ([Li and Durbin, 2009][2]), and GATK ([McKenna, et al., 2010][3]) for full functionality. The source code and compiled binaries are freely available from under a GNU General Public License. Benchmark comparisons demonstrate that ISG is faster and more flexible than comparable tools. [1]: #ref-3 [2]: #ref-8 [3]: #ref-9