FASTAQ-SCAFFOLDS_TO_CONTIGS(1)

✨ NAME ✨

fastaq_scaffolds_to_contigs — bestie, this is the one that makes a file of contigs out of a file of scaffolds 💖

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🌸 DESCRIPTION 🌸

okay so real talk, here's how you run it:

fastaq_scaffolds_to_contigs [options] <infile> <outfile>

What it does: it takes your scaffolds and gives you back contigs, no cap — meaning it breaks at every gap in the input. Every. Single. Gap. It's giving scissors energy ✂️✨

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🎀 positional arguments 🎀

• infile — the name of your input file, like the glow-up source material 🫶
• outfile — the name of your output contigs file, where the magic lands 💅

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💜 options 💜

• -h, --help — shows this help message and then bounces, exit stage left 👋
• --number_contigs — use this if you want your contig names enumerated 1, 2, 3, ... within each scaffold. Like, each scaffold gets its own lil count, starting fresh every time 💫 lowkey so tidy

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🫧 friendly reminder that this is literally all the options. short and sweet. iconic behaviour honestly.

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🌈 SEE ALSO 🌈

(no SEE ALSO section here bestie, this one's a standalone queen 👑)

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that's the whole page fr fr 🍓 — this was fastaq_scaffolds_to_contigs version 3...., dated January 2026, and it's part of the User Commands crew. go forth and de-scaffold, you absolute main character 🦋💖