RT Journal Article
SR Electronic
T1 Rapid Core-Genome Alignment and Visualization for Thousands of Intraspecific Microbial Genomes
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 007351
DO 10.1101/007351
A1 Todd J. Treangen
A1 Brian D. Ondov
A1 Sergey Koren
A1 Adam M. Phillippy
YR 2014
UL http://biorxiv.org/content/early/2014/07/22/007351.abstract
AB Though many microbial species or clades now have hundreds of sequenced genomes, existing whole-genome alignment methods do not efficiently handle comparisons on this scale. Here we present the Harvest suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial strains. Harvest includes Parsnp, a fast core-genome multi-aligner, and Gingr, a dynamic visual platform. Combined they provide interactive core-genome alignments, variant calls, recombination detection, and phylogenetic trees. Using simulated and real data we demonstrate that our approach exhibits unrivaled speed while maintaining the accuracy of existing methods. The Harvest suite is open-source and freely available from: http://github.com/marbl/harvest.