Download, install & run

harvest-tools is distributed as a precompiled binary. The three steps below represent the fastest way to start using the software:


On Linux:

Basic usage:

From command-line:

harvest-tools –x <input xmfa> -f <input reference fasta> -g <reference genbank formatted annotations> -n <newick formatted tree>

Advanced usage:

harvest-tools quick start for three example scenarios.

With reference & genbank file as input:

harvest-tools -g <reference_genbank_file1,reference_genbank_file2,..> -r <reference fasta file> -x <XMFA file> -o hvt.ggr

With harvest-tools file as input, XMFA output:

harvest-tools -i input.ggr -X output.xmfa

With harvest-tools file as input, fasta formatted SNP file as output:

harvest-tools -i input.ggr -S output.snps

Command-line parameters:

  • -b: <bed filter intervals>,<filter name>,”<description>”
  • -B: <output backbone intervals>
  • -f: <reference fasta>
  • -F: <reference fasta out>
  • -g: <reference genbank>
  • -h: (show this help)
  • -i: <harvest input>
  • -m: <multi-fasta alignment input>
  • -n: <Newick tree input>
  • -N: <Newick tree output>
  • –midpoint-reroot
  • -o: <hvt output>
  • -q: (quiet mode)
  • -S: <output for multi-fasta SNPs>
  • -v: <VCF input>
  • -V: <VCF output>
  • -x: <xmfa alignment file>
  • -X: <output xmfa alignment file>

Primary output files

  1. Compressed binary archive (GGR)