TO_FASTA.PY(1)

💖 NAME 💖

to_fasta.py — bestie, this is the glow-up machine that strips adapters off your reads and collapses your FASTQ into FASTA ✨

🦋 DESCRIPTION 🦋

okay so the way you run this, it's giving:

usage: to_fasta.py [-h] [-3 SEQ] [-5 SEQ] [--trim-5p BP] [--trim-3p BP]
              [--seed-5p BP] [--seed-3p BP] [-m BP] [-x BP] [-s] [-B] [-a]
              FASTQ

and what it does, in one breath: remove adapters and collapse reads from FASTQ to FASTA. that's the whole vibe. periodt 💅

🎀 positional arguments 🎀

• FASTQ — your input file, and yes she's flexible: this can also be stdin, or a compressed file in {zip,gz,tar,bz}. we love an adaptable icon 🫶

✨ optional arguments ✨

• -h, --help — shows this help message and then dips. classic. 😌
• -3 SEQ — the 3' adapter sequence, right there in the flesh 🌸
• -5 SEQ — the 5' adapter sequence, also right there 🌸
• --trim-5p BP — trim exactly this many bases off the 5' ends, no more no less 💅
• --trim-3p BP — same energy but for the 3' ends ✂️
• --seed-5p BP — how many bp of the 5' adapter we match against (default: 7) 👑
• --seed-3p BP — how many bp of the 3' adapter we match against (default: 7) 👑
• -m BP — minimum read length in bp (default: 16) 🍓
• -x BP — maximum read length in bp (default: 36) 🍓
• -s — sensitive adapter search, so it'll still catch a match with 1 mismatch (default: off) 🔥
• -B — only print the reads that have both a 5' and a 3' adapter match. picky queen behavior, we respect it 👑
• -a — print all reads, with and without adapter matches, as long as they land in the range you set with -m and -x. everyone gets an invite to this party 🌈

💜 AUTHOR 💜

this manpage was written by Andreas Tille for the Debian distribution, and bestie, it can be used for any other usage of the program too. no gatekeeping here 🫶

and that's the whole thing, no cap 🧚 this was to_fasta.py 1.1 from March 2020, mwah, go collapse some reads 💖✨