Quickstart

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 OSX:

1. wget ftp://ftp.cbcb.umd.edu/pub/software/harvest/harvesttools-OSX64.gz
2. tar -xvf harvesttools-OSX64.tar.gz

On Linux:

1. wget ftp://ftp.cbcb.umd.edu/pub/software/harvest/harvesttools-Linux64.gz
2. tar -xvf harvesttools-Linux64.tar.gz

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)