FASTAQ-FILTER(1)

🦋 FASTAQ-FILTER(1) 🦋

okay so bestie, welcome to section 1 (User Commands) and today's main character is fastaq_filter — bestie fr fr, she's the one who picks a lil subset of your sequences out of a whole file. let's GO 💅

---

✨ NAME ✨

fastaq_filter — filter sequences so you get a cute lil subset of them 🎀

---

🌸 DESCRIPTION 🌸

okay so here's the vibe, no cap:

usage: fastaq_filter [options] <infile> <outfile>

she filters a sequence file by sequence length and/or by name matching a regular expression. that's it, that's the whole job, and she ate 🔥

---

👑 OPTIONS 👑

🌈 positional arguments 🌈

• infile — the name of the input file that's getting filtered. this is your raw material bestie 💖
• outfile — the name of the output file. where the survivors go ✨

💜 options 💜

• -h, --help — shows this help message and dips, iconic behaviour honestly 🙈
• --min_length INT — the minimum length of sequence to keep. default is 0, so like, everything's invited to the party at first 🎉
• --max_length INT — the maximum length of sequence to keep. default is inf, aka infinity, aka no ceiling, sky's the limit bestie 🦋
• --regex REGEX — if you give her this, only the reads with a name matching the regular expression get kept. it's giving bouncer at the door energy 💅
• --ids_file FILENAME — if you give her this, only the reads whose ID is in the given file will be used. one ID per line of the file, so don't be doing anything cute with the formatting, okay? one. per. line. 📝
• -v, --invert — flips it 😭 only keeps the sequences that do NOT match the filters. the rejects become the chosen ones, main character energy fr

🫶 Mate file for read pairs options 🫶

• --mate_in FILENAME — the name of the mates input file. ⚠️ heads up: if you use this, you must also provide --mate_out, they're a package deal, they don't do long distance 😤
• --mate_out FILENAME — the name of the mates output file. the matching half of the deal above 💞
• --both_mates_pass — here's the tea: by default, if either mate passes the filter, then both reads get output. flip this flag on and you require that both reads of a pair pass the filter before either one goes through. strict queen behaviour 👑

lowkey important, bestie: the default mate behaviour is either one passes → both get written out. only reach for --both_mates_pass if you genuinely want the stricter "both or nothing" rule. no cap 🧚

---

and that's the whole page, you're basically a bioinformatics girlie now 🌸✨

this was the fastaq_filter manual, version 3.17.0, from January 2026 — mwah, go filter something cute 💖🎀🌈