FASTAQ-CHUNKER(1)

✨ NAME ✨

fastaq_chunker — splits sequences into equal sized chunks 🧚 (yes bestie, that's the whole vibe: chop chop, evenly)

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💖 DESCRIPTION 💖

okay so first things first, the usage, and it is literally this and nothing else:

fastaq_chunker [options] <infile> <out> <chunk size> <tolerance>

So what does it DO? It splits a multi sequence file into separate files, and it splits those sequences into chunks of a fixed size. The way it works: it aims for chunk_size chunks in each file, but it lowkey allows a little extra, so a chunk can be up to (chunk_size + tolerance). Why? to prevent tiny chunks made from the ends of sequences 🫶 like, nobody wants a sad little leftover crumb chunk, it's giving unacceptable.

🎀 positional arguments 🎀

• infile — Name of input file to be split. your main character file 💅
• out — Prefix of output file. not me making this confusing but: if --onefile is used, then this is the name of the single output file instead 👑
• chunk_size — Size of each chunk. the goal, the dream, the number ✨
• tolerance — Tolerance allowed in chunk size. the wiggle room, the grace, the slay 🌸

💅 options 💅

• -h, --help — show this help message and exit (the classic, the icon, the escape hatch 🙈)
• --onefile — Output all the sequences in one file. one file, one vibe, no splitting into a million lil guys 🌈
• --skip_all_Ns — Do not output any sequence that consists of all Ns. if it's all Ns we simply do not see it, no cap 💀

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and that's the whole page bestie, you ate it 💖 this was fastaq_chunker version 3.17.0, from January 2026, and yes the manual page header was giving FASTAQ-CHUNKER(1) the entire time, slay 🎀✨