harvesttools(1) archiving and postprocessing for reference-compressed genomic multi-alignments


harvesttools <options>


Harvesttools is a utility for creating and interfacing with Gingr files, which are efficient archives that the Harvest Suite uses to store reference-compressed multi-alignments, phylogenetic trees, filtered variants and annotations. Though designed for use with Parsnp and Gingr, HarvestTools can also be used for generic conversion between standard bioinformatics file formats.


-i <Gingr input>
-b <bed filter intervals>,<filter name>,"<description>"
-B <output backbone intervals>
-f <reference fasta>
-F <reference fasta out>
-g <reference genbank>
-a <MAF alignment input>
-m <multi-fasta alignment input>
-M <multi-fasta alignment output (concatenated LCBs)>
-n <Newick tree input>
-N <Newick tree output>
--midpoint-reroot (reroot the tree at its midpoint after loading)
-o <Gingr output>
-S <output for multi-fasta SNPs>
-u 0/1 (update the branch values to reflect genome length)
-v <VCF input>
-V <VCF output>
-x <xmfa alignment file>
-X <output xmfa alignment file>
-h (show this help)
-q (quiet mode)


This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.