FASTQ-INTERLEAVE(1)

💖 FASTQ-INTERLEAVE 💖

okay bestie, buckle up, because this little fastq-interleave baddie is about to become your new favorite thing in the whole entire world of bioinformatics ✨ it lives in the User Commands section of the manual (section 1, no cap), and honestly? it's giving "small tool, huge main character energy" 🎀

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🌸 NAME 🌸

fastq-interleave — read 2 fastq files, and write them interleaved 🦋

that's it. that's the whole job. two files in, one gorgeous interleaved file out. iconic behavior, truly. 💅

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✨ SYNOPSIS ✨

fastq-interleave x.fastq y.fastq
fastq-interleave x.fastq.gz y.fastq.gz

so you literally just hand it your two files, okay? like:

fastq-interleave x.fastq y.fastq

and if your files are all gzipped and cute (as they should be, we love compression here 🫶) then:

fastq-interleave x.fastq.gz y.fastq.gz

that's the vibe. no complicated flag soup, no reading a 40-page wiki at 2am. just two file args and you're done. periodt. 👑

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💜 DESCRIPTION 💜

okay so here's the tea, bestie ☕️ — fastq-interleave reads 2 fastq files and writes them out interleaved. that means the reads from both files get woven together into one single output stream, so instead of having your mate 1 reads chilling in one file and your mate 2 reads in another, they're all snuggled up together, alternating. so cozy. so convenient. 😭

now for the ✨header✨ of the situation — this tool keeps just the first word of header lines. literally just the first word, okay? the rest of the descriptive stuff after the first whitespace? gone. not invited to the party. 🙈

and here's the cute little detail that makes my heart sing: if the two header lines are otherwise identical, it appends /1 and /2 to them respectively. so your read pairs stay labeled and distinguishable. chef's kiss. 🤌

⚠️ and now for the important part, so listen up: this whole thing assumes 1 fastq per 4 lines, i.e. no line wrapping. if your fastq files are wrapped (why would you do that to yourself, bestie 💀), this tool is not gonna have a good time. four lines = one fastq record. that's the whole math. no exceptions.

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🫶 a lil sign-off 🫶

okay that's the entire manual, you're officially educated ✨ this page is for fastq-interleave, version 1654, and it's dated August 2026 📅 so yeah — go interleave something, slay, and remember: four lines per read, no wrapping, and you'll be fine. mwah 💖🎀🦋🌸