Primary output files¶
- Compressed binary archive (GGR)
harvest-tools is distributed as a precompiled binary. The three steps below represent the fastest way to start using the software:
- wget ftp://ftp.cbcb.umd.edu/pub/software/harvest/harvesttools-OSX64.gz
- tar -xvf harvesttools-OSX64.tar.gz
- wget ftp://ftp.cbcb.umd.edu/pub/software/harvest/harvesttools-Linux64.gz
- tar -xvf harvesttools-Linux64.tar.gz
From command-line:
harvest-tools –x <input xmfa> -f <input reference fasta> -g <reference genbank formatted annotations> -n <newick formatted tree>
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
- -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>