Work

The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes

Year: 2014

Type: article

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.

Source: Genome biology

DOI: 10.1186/preaccept-2573980311437212

Authors: Todd J Treangen, Brian D Ondov, Sergey Koren, Adam M Phillippy

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $5,490

Funders: U.S. Department of Homeland Security, Battelle, Science and Technology Directorate

Awards: G1093785223, G5116269224