Neptune: a bioinformatics tool for rapid discovery of genomic variation in bacterial populations.

Marinier E1, Zaheer R1, Berry C1, Weedmark KA1, Domaratzki M2, Mabon P1, Knox NC1, Reimer AR1, Graham MR1,3, Chui L4,5, Patterson-Fortin L5, Zhang J6, Pagotto F7, Farber J7, Mahony J8, Seyer K9, Bekal S10,11, Tremblay C10,11, Isaac-Renton J12, Prystajecky N12,13, Chen J14, Slade P15, Van Domselaar G1,3.

Author information

Abstract

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 datasets 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. The software is available for download at: http://github.com/phac-nml/neptune.

PMID:

29048594

DOI:

10.1093/nar/gkx702