# Rapid Core-Genome Alignment and Visualization for Thousands of Microbial Genomes

## TL;DR

The Harvest suite offers fast and accurate tools for aligning and visualizing thousands of microbial genomes.

## Contribution

Harvest introduces a new suite of tools for rapid and accurate large-scale microbial genome analysis.

## Key findings

- Harvest demonstrates unrivaled speed in core-genome alignment while maintaining accuracy.
- The suite includes tools for variant calling, recombination detection, and phylogenetic tree generation.
- Both simulated and real data validate the effectiveness of the Harvest approach.

## Abstract

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.