TY - JOUR T1 - Rapid Core-Genome Alignment and Visualization for Thousands of Intraspecific Microbial Genomes JF - bioRxiv DO - 10.1101/007351 SP - 007351 AU - Todd J. Treangen AU - Brian D. Ondov AU - Sergey Koren AU - Adam M. Phillippy Y1 - 2014/01/01 UR - http://biorxiv.org/content/early/2014/07/22/007351.abstract N2 - 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. ER -