HARVESTTOOLS(1)

💖 HARVESTTOOLS(1) 💖

okay bestie, gather round, because this is harvesttools — a User Commands girly from the Harvest Suite family, and she is booked and busy. ✨

🌸 NAME 🌸

harvesttools — archiving and postprocessing for reference-compressed genomic multi-alignments 🧬💅

🦋 SYNOPSIS 🦋

harvesttools <options>

✨ DESCRIPTION ✨

So Harvesttools is this utility for creating and interfacing with Gingr files, and Gingr files are these super efficient archives that the Harvest Suite uses to store reference-compressed multi-alignments, phylogenetic trees, filtered variants, and annotations. iconic behavior honestly. 👑

And like — yes she was designed for use with Parsnp and Gingr, that's her whole origin story, but plot twist: HarvestTools can also be used for generic conversion between standard bioinformatics file formats. versatile queen. no cap. 🫶

💅 OPTIONS 💅

one bullet per flag, no skipping, we don't gatekeep here:

• -i <Gingr input> — your Gingr file going in 🍓
• -b <bed filter intervals>,<filter name>,"<description>" — bed filter intervals, then the filter name, then a quoted description. yes, all three, comma-separated, she's specific 💀
• -B <output backbone intervals> — where the backbone intervals go out
• -f <reference fasta> — reference fasta in
• -F <reference fasta out> — reference fasta out
• -g <reference genbank> — reference genbank, right this way
• -a <MAF alignment input> — MAF alignment coming in
• -m <multi-fasta alignment input> — multi-fasta alignment coming in
• -M <multi-fasta alignment output (concatenated LCBs)> — multi-fasta alignment going out, and it's the concatenated LCBs version, noted 📝
• -n <Newick tree input> — Newick tree in 🌳
• -N <Newick tree output> — Newick tree out 🌳
• --midpoint-reroot — reroot the tree at its midpoint after loading. that's it, that's the whole job 🎯
• -o <Gingr output> — your Gingr file going out
• -S <output for multi-fasta SNPs> — where the multi-fasta SNPs land
• -u 0/1 — update the branch values to reflect genome length. it takes a 0 or a 1, pick your fighter
• -v <VCF input> — VCF in
• -V <VCF output> — VCF out
• -x <xmfa alignment file> — xmfa alignment file in
• -X <output xmfa alignment file> — xmfa alignment file out
• -h — show this help. hi, hello, here's the help 🫶
• -q — quiet mode 🤫

ngl bestie, that's the whole list — 20 options, every single one accounted for. count them if you want, I'll wait. 💖

🎀 AUTHOR 🎀

This manpage was written by Andreas Tille for the Debian distribution, and can be used for any other usage of the program. shoutout Andreas, thank you for your service 🙏✨

and that's the whole vibe check, bestie — harvesttools version 1.2, dated March 2016, slaying since day one. periodt. 💅👑