SSAKE(1)

💖 SSAKE — the iconic one 💖

okay bestie, welcome to ssake(1), a General Commands Manual situation, and honestly? this page is giving "assemble millions of very short DNA sequences" and it is not playing around. grab a strawberry 🍓, sit down, we're doing bioinformatics.

✨ NAME ✨

ssake — assembling millions of very short DNA sequences 🧬

🦋 SYNOPSIS 🦋

Progressive assembly of millions of short DNA sequences by k-mer search
through a prefix tree and 3' extension.

that's it. that's the whole vibe. a prefix tree and a 3' extension, main character energy only. ✨

🎀 OPTIONS 🎀

• -f — the Fasta file holding all your reads, either paired (-p 1) or unpaired (-p 0). this one is required, no cap. and heads up, bestie: if your reads are paired, they now have to be separated by ":" 🫶
• -s — a Fasta file of sequences to use as seeds exclusively. only specify this if it's different from your read set. optional, iykyk 🌸
• -m — minimum number of overlapping bases with the seed/contig while the overhang consensus is being built up (default -m 16) 🧵
• -o — minimum number of reads needed before a base gets called during an extension (default -o 3) 🗳️
• -r — minimum base ratio used to accept an overhang consensus base (default -r 0.7) 💯
• -t — trim up to -t base(s) off the contig end once every possibility for an extension has been exhausted (default -t 0) ✂️
• -p — are we doing paired-end reads? (-p 1 = yes, -p 0 = no, default -p 0) 👯
• -v — runs in verbose mode (-v 1 = yes, -v 0 = no, default -v 0, optional) 📢
• -b — base name for your output files (optional) 📁

============ options below are only considered with -p 1 ============ 💅

so like. everything past this line only matters if you said -p 1. fr fr.

• -d — mean distance you expect / observed between paired-end reads (default -d 200, optional) 📏
• -e — error (%) allowed on that mean distance. e.g. -e 0.75 == distance +/- 75% (default -e 0.75, optional) 🎯
• -k — minimum number of links (read pairs) needed to compute a scaffold (default -k 2, optional) 🔗
• -a — maximum link ratio between the two best contig pairs. higher values lead to least accurate scaffolding (default -a 0.70, optional) 🚨

not me warning you: crank -a up and your scaffolding gets less accurate. the manpage literally said so, I'm just being dramatic about it. 🙈

• -z — minimum contig size for tracking paired-end reads (default -z 50, optional) 📐
• -g — a Fasta file containing unpaired sequence reads (optional) 🌈

👑 SEE ALSO 👑

/usr/share/doc/ssake/SSAKE.readme between

💜 AUTHORS 💜

this manual page was written by Andreas Tille <tille@debian.org> for the Debian system (but it may be used by others, she's generous like that 💖). Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 or any later version published by the Free Software Foundation.

on Debian systems, the complete text of the GNU General Public License lives at /usr/share/common-licenses/GPL.

and that's the whole page, bestie — ✨ January 2008, from the SSAKE(1) era, and it still ate. periodt. 💅🎀🦋