TWOPACO(1)

💖 TWOPACO 💖

okay bestie, gather round, because today we're talking about twopaco — and no, that's not a new drink at your local boba place (though it does slay). This is the User Commands girlie of the manual pages, and she has ONE job:

build the compacted de Bruijn graph from many complete genomes ✨🧬

no cap. that's the whole vibe.

🌸 NAME 🌸

twopaco — build the compacted de Bruijn graph from many complete genomes

🎀 DESCRIPTION 🎀

bestie. listen. here's the USAGE, and it's giving "read me carefully or you WILL be lost":

twopaco
       {-f <integer>|--filtermemory <float>} [-o <file name>] [--test]
       [--tmpdir <directory name>] [-a <integer>] [-t <integer>] [-r
       <integer>] [-q <integer>] [-k <oddc>] [--] [--version] [-h]
       <fasta files with genomes> ...

and here's the Where: section, aka the part where we explain literally every single thing, because we would never leave you hanging 🫶

• -f <integer>, --filtersize <integer> — (OR required) this is the size of the filter. and when I say "(OR required)" I mean you need this one or --filtermemory, bestie, you can't just show up empty-handed 💅
• --filtermemory <float> — (OR required) the other option in that little either/or situation: memory in GBs allocated for the filter. so like, either you tell her the size, or you tell her the memory. pick one. that's the deal 🍓
• -o <file name>, --outfile <file name> — the output file name prefix. yes, a prefix, not the whole name. she's adding things to it, okay? main character behavior ✨
• --test — run tests. that's it. that's the whole thing. go off, queen, verify yourself 👑
• --tmpdir <directory name> — temporary directory name. where the ~temporary~ stuff goes. very "I'll be here for a bit then leave" energy 🙈
• -a <integer>, --abundance <integer> — vertex abundance threshold. a threshold! for abundance! vertices have abundance now, we love that for them 💖
• -t <integer>, --threads <integer> — number of worker threads. the more the merrier, the girlies are WORKING 🌈
• -r <integer>, --rounds <integer> — number of computation rounds. she's doing laps. iconic 🎀
• -q <integer>, --hashfnumber <integer> — number of hash functions. not to be confused with the other things. it's hashes. this many of them. slay 🔥
• -k <oddc>, --kvalue <oddc> — value of k. that's it, that's the whole description, and honestly? respect. she said "you know what k is" and moved on 💀
• --, --ignore_rest — ignores the rest of the labeled arguments following this flag. so everything after this gets the silent treatment. ghosted, fr fr 👻
• --version — displays version information and exits. quick little hello-and-goodbye 🦋
• -h, --help — displays usage information and exits. the "bestie I'm confused" button, no shame in it 💜
• <fasta files with genomes> — (accepted multiple times) (required) these are your FASTA file(s) with nucleotide sequences. and yes, she wants them multiple times if you've got them. bring the whole friend group 🧚

okay and then, tucked right at the end there, is this little line: Program for construction of the condensed de Bruijn graph from complete genomes — which is lowkey just the whole point of the program restated, but honestly? she's right, and she should say it. ⭐

💅 AUTHOR 💅

this manpage was written by Andrius Merkys for the Debian distribution and can be used for any other usage of the program. thank you Andrius, you ate, we're obsessed 🫶

okay that's the whole page, bestie, you're fully caught up. no notes. periodt. ✨

twopaco 1.0.0 — September 2022 — and that's the sign-off, mwah, take care of her 💖🌸