Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes. Harvest includes: Parsnp, a fast core-genome multi-aligner, Gingr, a dynamic visual platform, and harvest-tools, providing both a reference compressed binary archive and format conversion tools.

##Release status

08/08/14: v1.0.1

##Harvest suite download:

• OSX (10.7 or newer):
  • https://github.com/marbl/harvest/releases/download/v1.0.1/harvest-OSX64-v1.0.1.tar.gz
  • MD5 sum: 86df3afe4ea61f5799bd4dfdf18087e9
• Linux/*nix:
  • https://github.com/marbl/harvest/releases/download/v1.0.1/harvest-Linux64-v1.0.1.tar.gz
  • MD5 sum: a6227d26b5c94a9904039c3e67a160cf

##Harvest suite documentation (in prep):

• http://harvest.readthedocs.org/en/latest/

##Individual Harvest components:

1. Parsnp

• Description: core genome aligner
• Project url: http://github.com/marbl/parsnp
• Language: C, C++, Python
• OSX prebuilt binary:
  • https://github.com/marbl/parsnp/releases/download/v1.0/parsnp-OSX64-v1.0.tar.gz
  • MD5 sum: 08c19b4d12e8199b2ce098550b4100e6
• Linux prebuilt binary:
  • https://github.com/marbl/parsnp/releases/download/v1.0/parsnp-Linux64-v1.0.tar.gz
  • MD5 sum: f82b6b9dae456fe9263ee6214b2633af

2. Gingr

• Description: GUI, interactive visualization of multiple alignments, phylogenies and variants (SNPs etc)
• Gingr is able to display:
  • Newick formatted trees
  • XMFA formatted multi-alignments (with synteny view)
  • VCF formatted variants
  • Harvest tools GGR format
• Project url: http://github.com/marbl/gingr
• Language: C++
• OSX prebuilt binary:
  • https://github.com/marbl/gingr/releases/download/v1.0.1/gingr-OSX64-v1.0.1.zip
  • MD5 sum: 455ebd0b68e064b1fd5b18decfc49905
• Linux prebuilt binary:
  • https://github.com/marbl/gingr/releases/download/v1.0.1/gingr-Linux64-v1.0.1.tar.gz
  • MD5 sum: 386dee47f6be86367e7ab92ad1334ef1

3. Harvest tools

• Description: binary format and conversion utilities
• Project url: http://github.com/marbl/harvest-tools
• Language: C++, Python
• OSX prebuilt binary:
  • https://github.com/marbl/harvest-tools/releases/download/v1.0.1/harvesttools-OSX64-v1.0.1.tar.gz
  • MD5 sum: bbc75536d40b02e597589e55df189235
• Linux prebuilt binary:
  • https://github.com/marbl/harvest-tools/releases/download/v1.0.1/harvesttools-Linux64-v1.0.1.tar.gz
  • MD5 sum: 48386692d434bbc947ea0058e95b2f15