@article {Marinier032227, author = {Eric Marinier and Rahat Zaheer and Chrystal Berry and Kelly Weedmark and Michael Domaratzki and Philip Mabon and Natalie Knox and Aleisha Reimer and Morag Graham and The Canadian Listeria Detection and Surveillance using Next Generation Genomics (LiDS-NG) Consortium {\textdagger} and Gary Van Domselaar}, title = {Neptune: A Tool for Rapid Microbial Genomic Signature Discovery}, elocation-id = {032227}, year = {2016}, doi = {10.1101/032227}, publisher = {Cold Spring Harbor Laboratory}, abstract = {Neptune locates genomic signatures using an exact k-mer matching strategy while accommodating k-mer mismatches. The software identifies sequences that are sufficiently represented within {\textquotedblleft}inclusion targets{\textquotedblright} and sufficiently absent from {\textquotedblleft}exclusion targets{\textquotedblright}. The signature discovery process is accomplished using probabilistic models instead of heuristic strategies. We have evaluated Neptune on Listeria monocytogenes and Escherichia coli genome data sets and found that signatures identified from these experiments are sensitive and specific to their respective data sets. In addition, the identified loci provide a catalog of differential loci for research of group-specific traits. Neptune has broad implications in microbial characterization for public health applications due to its efficient ad hoc signature discovery based upon differential genomics.}, URL = {https://www.biorxiv.org/content/early/2016/01/08/032227}, eprint = {https://www.biorxiv.org/content/early/2016/01/08/032227.full.pdf}, journal = {bioRxiv} }