FASTAQ-TO_PERFECT_READS(1)

✨ fastaq_to_perfect_reads(1) — the manual page, but make it cute ✨

okay bestie, welcome to fastaq_to_perfect_reads. it's a little user command that lives in the fastaq family and it's literally here to make you perfect paired reads from a reference. no cap. let's get into it 💅

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🌸 NAME 🌸

fastaq_to_perfect_reads — make perfect paired reads from a reference 🧚

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💖 DESCRIPTION 💖

here's the vibe, the whole usage in one breath:

fastaq_to_perfect_reads [options] <infile> <outfile> <mean insert
size> <insert std deviation> <mean coverage> <read length>

so what does it do? it makes perfect paired end fastq reads from a sequence file, and the insert sizes get sampled from a normal distribution. periodt.

and the read orientation is innies 🫶 (iykyk). the output is an interleaved FASTQ file, so both mates of a pair are chillin' in the same file, one after the other. iconic behaviour honestly.

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👑 positional arguments 👑

these are the six things you gotta hand over, in this order:

• infile — the name of the input file 📥
• outfile — the name of the output file 📤
• mean insert size — the mean insert size of the read pairs 📏
• insert std deviation — the standard devation of the insert size (yes girl, "devation" is the original's spelling, not mine 💀)
• mean coverage — the mean coverage of the reads 🔥
• read length — the length of each read ✂️

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✨ options ✨

flip through these, pick your faves, slay:

• -h, --help — shows this help message and exits. the classic. the goat. 👑
• --fragments FILENAME — writes FASTA sequences of the fragments (that's the read pairs plus the sequences in between them) to the filename you give it 💾
• --no_n — don't allow any N or n characters in the reads. not even one. not even lowercase. 🚫
• --seed INT — seed for the random number generator. default is to use python's default 🎲

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💀 quick note bestie: there's no other flags hiding in here. what you see is what you get, and that's on periodt.

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🎀 the sign-off 🎀

this little baddie is fastaq_to_perfect_reads version 3.17.0, dated January 2026. go forth and make perfect reads, my love 🌈💜