FASTAQ-ADD_INDELS(1)

✨ fastaq-add_indels — the manual page, but make it cute ✨

okay bestie, welcome to fastaq-add_indels from the FASTAQ-ADD_INDELS(1) user commands era 💖 it's a lil command-line tool and honestly? it does exactly two things and it does them iconically. it deletes or inserts bases at given position(s). that's it, that's the whole personality 💅

---

🌸 NAME 🌸

fastaq_add_indels — deletes or inserts bases at given position(s). that's the vibe. no cap 🦋

---

🎀 DESCRIPTION 🎀

here's how you summon it, fr fr:

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

and again, for the people in the back: it deletes or inserts bases at given position(s). give it a file, tell it where to mess with the bases, get a file back. main character energy honestly 👑

💜 positional arguments:

so you gotta give it two things, no skipping, periodt:

• infile — name of the input file. the source, the blueprint, the origin story 🍼
• outfile — name of the output file. where your freshly edited sequences get to live their best life ✨

🫶 options:

okay this is the good part. look at all these flags, we love a menu 🍓

• -h, --help — shows this help message and dips. exit stage left, goodbye 🙈
• -d, --delete Name:start:bases — delete the given bases from the given sequence. the format is the same as samtools view: name:start-end. and listen, you can use this option multiple times — once for each region you wanna delete. also, overlapping coords get merged before deleting, so don't stress about duplicates, it's got you 💖
• --delete_range P,start,step — deletes bases starting at position P in each sequence of the input file. it deletes start + (n-1)*step bases from sequence n. yes queen, the maths scales per sequence, slay 📐
• -i, --insert Name:start:bases — insert a random string of bases at the given position. format is name:position:number_to_add, and the bases get added after the position. use it multiple times if you're feeling extra 💅
• --insert_range P,start,step — inserts random bases starting after position P in each sequence of the input file. it inserts start + (n-1)*step bases into sequence n. random bases, but make it systematic 🌈

---

lowkey important bestie: -d/--delete and -i/--insert are both repeatable — stack them as many times as you want, one per region. that's not me being dramatic, that's literally in the spec 🎀

---

⭐ SEE ALSO ⭐

nothin' listed in this page, so just go forth and edit some bases, iykyk 🦋

---

that's the whole page, you made it to the end, iconic behavior honestly 👑 this was fastaq_add_indels version 3.17.0, dated January 2026 — go get 'em, and remember: the bases don't delete themselves 💖✨🧚