title: The Harvest suite for rapid core-genome  alignment and visualization of thousands of  intraspecific microbial genomes.
abstract: Whole-genome sequences are now available for many microbial species and clades, however existing whole-genome alignment methods are limited in their ability to perform sequence comparisons of multiple sequences simultaneously. Here we present the Harvest suite of core-genome alignment and visualization tools for the rapid and simultaneous analysis of thousands of intraspecific microbial strains. Harvest includes Parsnp, a fast core-genome multi-aligner, and Gingr, a dynamic visual platform. Together 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.
authors.forename: Todd J
authors.initials: TJ
authors.lastname: Treangen
authors.forename: Brian D
authors.initials: BD
authors.lastname: Ondov
authors.forename: Sergey
authors.initials: S
authors.lastname: Koren
authors.forename: Adam M
authors.initials: AM
authors.lastname: Phillippy
mesh_terms: D000465:Algorithms; D001419:Bacteria / Q000235:genetics*; D016680:Genome, Bacterial / Q000235:genetics*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012984:Software