Harvest

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, and Gingr, a dynamic visual platform. Combined they provide interactive core-genome alignments, variant calls, recombination detection, and phylogenetic trees.

Harvest components

1. Harvest tools

   -->binary format and conversion utilities

2. Gingr

   -->GUI, interactive visualization of alignments, trees and variants


3. Parsnp

   -->multiple core genome alignment, SNP filtration, core genome phylogeny

Documentation on readthedocs

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

Latest release and source code on github

• http://github.com/marbl/harvest

Parsnp binaries used in manuscript (v1.0)

• OSX: download
• LINUX: download

Experimental results

1. Dataset #1: 32 simulated E. coli W3110 strains
   • Low mutation rate: assemblies | reads
     • BWA results: VCF
     • kSNP results: VCF
     • Mauve results: XMFA
     • Mugsy results: MAF
     • Parsnp results: VCF
     • Smalt results: VCF
     • Known truth: VCF
   • Medium mutation rate: assemblies | reads
     • BWA results: VCF
     • kSNP results: VCF
     • Mauve results: XMFA
     • Mugsy results: MAF
     • Parsnp results: VCF
     • Smalt results: VCF
     • Known truth: VCF
   • High mutation rate: assemblies | reads
     • BWA results: VCF
     • kSNP results: VCF
     • Mauve results: XMFA
     • Mugsy results: MAF
     • Parsnp results: VCF
     • Smalt results: VCF
     • Known truth: VCF
   • Rearrangement script: download

• Dataset #2: 826 P. difficile genomes
  • Gingr input format: GGR
  • Newick formatted phylogeny: TREE
  • XMFA formatted alignment: XMFA

• Dataset #3: 224 M. tuberculosis genomes
  • Gingr input format: GGR
  • Newick formatted phylogeny: TREE
  • XMFA formatted alignment: XMFA
  • Common SNP calls VCF

• Dataset #4: 31 S. pneumoniae TIG4 genomes
  • Gingr file: download
  • XMFA formatted alignment: download
• Dataset #5: 10,000 simulated S. pneumoniae TIG4 strains
  • Tarball of genomes: download