PT  - JOURNAL ARTICLE
AU  - Eric Marinier
AU  - Rahat Zaheer
AU  - Chrystal Berry
AU  - Kelly Weedmark
AU  - Michael Domaratzki
AU  - Philip Mabon
AU  - Natalie Knox
AU  - Aleisha Reimer
AU  - Morag Graham
AU  - Linda Chui
AU  - The Canadian Listeria Detection and Surveillance using Next Generation Genomics (LiDS-NG) Consortium
AU  - Gary Van Domselaar
TI  - Neptune: A Bioinformatics Tool for Rapid Discovery of Genomic Variation in Bacterial Populations
AID  - 10.1101/032227
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 032227
4099  - http://biorxiv.org/content/early/2016/11/30/032227.short
4100  - http://biorxiv.org/content/early/2016/11/30/032227.full
AB  - The ready availability of vast amounts of genomic sequence data has created the need to rethink comparative genomics algorithms using “big data” approaches. Neptune is an efficient system for rapidly locating differentially abundant genomic content in bacterial populations using an exact k-mer matching strategy, while accommodating k-mer mismatches. Neptune’s loci discovery process identifies sequences that are sufficiently common to a group of target sequences and sufficiently absent from non-targets using probabilistic models. Neptune uses parallel computing to efficiently identify and extract these loci from draft genome assemblies without requiring multiple sequence alignments or other computationally expensive comparative sequence analyses. Tests on simulated and real data sets showed that Neptune rapidly identifies regions that are both sensitive and specific. We demonstrate that this system can identify trait-specific loci from different bacterial lineages. Neptune is broadly applicable for comparative bacterial analyses, yet will particularly benefit pathogenomic applications, owing to efficient and sensitive discovery of differentially abundant genomic loci.