FASTAQ-CAPILLARY_TO_PAIRS(1)

💖 NAME 💖

fastaq_capillary_to_pairs — converts a file of capillary reads into paired and unpaired files, like the multitasking queen she is. 👑

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🦋 DESCRIPTION 🦋

okay so, bestie, the vibe check on this one is literally:

fastaq_capillary_to_pairs <infile> <outfiles prefix>

Give it a file of capillary reads and it goes off and makes two things for you:

the way that it makes an interleaved file of read pairs — and when there's more than one read from the same ligation, it takes the longest read, no drama, no tiebreak chaos — and then also a whole separate file of unpaired reads. Everyone's accounted for. 🤝

And the little name glow-up?? It replaces the .p1k/.q1k part of read names with /1 and /2 to denote fwd/rev reads. that's it, that's the transformation. iconic behaviour honestly. ✨

🌸 positional arguments 🌸

• infile — Name of input fasta/q file. the whole point of the operation, lowkey.
• outfiles prefix — Prefix of output files. you pick the prefix, it builds the files off that. 🫶

🎀 options 🎀

• -h, --help — show this help message and exit. the classic escape hatch, always there for you. 💅

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ngl if you were hoping for a flag buffet, this page is a light snack — that's genuinely all the options. also remember: <infile> and <outfiles prefix> are both required, so no leaving them out. fr fr.

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that's the whole manual, bestie 🦋 go convert some capillary reads and be the main character of your own assembly pipeline ✨

— with love, fastaq_capillary_to_pairs 3.17.0, January 2026, straight out of the User Commands manual 💜