FASTAQ-SEQUENCE_TRIM(1)

✨ FASTAQ-SEQUENCE_TRIM ✨

okay bestie, welcome to fastaq_sequence_trim, from section 1 of the User Commands manual 💅

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🎀 NAME 🎀

fastaq_sequence_trim — trim exact matches to a given string off the start of every sequence ✂️✨

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📖 DESCRIPTION 📖

usage, babes:

fastaq_sequence_trim [options] <infile_1> <infile_2> <outfile_1> <outfile_2> <trim_seqs>

so the vibe is: it trims sequences off the start of all sequences in a pair of sequence files, whenever there is a perfect match 🎯 no match, no trim, periodt.

and here's the important part — it only keeps a read pair if both reads of the pair are at least a minimum length after any trimming 👑 so if one read gets chopped too short, that whole pair is out. no half-pairs up in here 🙈

🦋 positional arguments 🦋

• infile_1 — the name of the forward fasta/q file you wanna trim 💖
• infile_2 — the name of the reverse fasta/q file you wanna trim 💖
• outfile_1 — the name of the output forward fasta/q file 🌸
• outfile_2 — the name of the output reverse fasta/q file 🌸
• trim_seqs — the name of a file of sequences to search for at the start of each input sequence 🔍 like, these are the things it's hunting for at the beginning of every read, iykyk

⚙️ options ⚙️

• -h, --help — show this help message and exit 🫶 classic, iconic, always there for u
• --min_length INT — minimum length of output sequences, default is [50] 📏
• --revcomp — trim the end of each sequence if it matches the reverse complement 🧬 this option is intended for PCR primer trimming, so if that's ur era, this is ur flag 🔥

bestie reminder: with --revcomp it's the end getting trimmed, not the start — two ends, two jobs, don't mix them up 💀

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that's the whole thing, no cap 💜 go trim something, slay.

fastaq_sequence_trim 3.17.0 · January 2026 — mwah, made with love, see u next manpage 🎀🦋💖