PT  - JOURNAL ARTICLE
AU  - Jason W. Sahl
AU  - Stephen M. Beckstrom-Sternberg
AU  - James S. Babic-Sternberg
AU  - John D. Gillece
AU  - Crystal M. Hepp
AU  - Raymond K. Auerbach
AU  - Waibhav Tembe
AU  - David M. Wagner
AU  - Paul S. Keim
AU  - Talima Pearson
TI  - The I<em>n</em> S<em>ilico</em> Genotyper (ISG): an open-source pipeline to rapidly identify and annotate nucleotide variants for comparative genomics applications
AID  - 10.1101/015578
DP  - 2015 Jan 01
TA  - bioRxiv
PG  - 015578
4099  - http://biorxiv.org/content/early/2015/02/20/015578.short
4100  - http://biorxiv.org/content/early/2015/02/20/015578.full
AB  - 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.