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

07/21/14: v1.0

##Harvest suite download:

• OSX (10.7 or newer):
  • https://github.com/marbl/harvest/releases/download/v1.0/harvest-OSX64.tar.gz
  • MD5 sum: 31c2af7272897fd1926758a4e9399e46
• Linux/*nix:
  • https://github.com/marbl/harvest/releases/download/v1.0/harvest-Linux64.tar.gz
  • MD5 sum: 170b054d6c5656df64e5c9f2c8c4072c

##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.gz
  • MD5 sum: 08c19b4d12e8199b2ce098550b4100e6
• Linux prebuilt binary:
  • https://github.com/marbl/parsnp/releases/download/v1.0/parsnp-Linux64.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/gingr-OSX64.app.zip
  • MD5 sum: 84c8d3818b48656132b5adf9a125783d
• Linux prebuilt binary:
  • https://github.com/marbl/gingr/releases/download/v1.0/gingr-Linux64.gz
  • MD5 sum: 3e4fdab0319be4c927b8738c2223f15b

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/harvesttools-OSX64.gz
  • MD5 sum: 4cc638e05c82bab24f2f68317347661e
• Linux prebuilt binary:
  • https://github.com/marbl/harvest-tools/releases/download/v1.0/harvesttools-Linux64.gz
  • MD5 sum: 4f41d17dd49eb8be7861a0325bed9910