REAPR-BREAK(1)

💖 REAPR-BREAK(1) 💖

okay so bestie, welcome to reapr-break — the part of REAPR that goes snap 🔥

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✨ NAME ✨

reapr-break — make broken assembly via REAPR 🫶

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🌸 SYNOPSIS 🌸

reapr break [options] <assembly.fa> <errors.gff.gz> <outfileprefix>

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🦋 DESCRIPTION 🦋

so like, <errors.gff.gz>?? that's the errors GFF file you get when you run score. that's it. that's the tea ☕ she takes it and she breaks things (the assembly, specifically, on purpose, which is iconic of her honestly 💅).

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👑 OPTIONS 👑

• -a — aggressive breaking mode, no cap 💥 she breaks contigs at any FCD or low_frag error, instead of the default behaviour where those just get replaced with Ns. each contig gets broken at the midpoint of each error. also check out -t while you're here. incompatible with -b (they cannot be in the same room, it's giving nemesis energy 😭).
• -b — she ignores FCD and low fragment coverage errors that do not contain a gap (the default is to replace those ones with Ns). incompatible with -a, fr fr.
• -e <float> — minimum FCD error [0]
• -l <int> — minimum sequence length to output [100]
• -m <int> — max sequence length to write to the bin 🗑️. sequences longer than this go to the main assembly output instead. this exists to stop long stretches of sequence from getting lost [999] — protective queen behaviour, we love her 🎀
• -t <int> — when -a is in play, use this one to say how many bases get trimmed off the end of each new contig around a break. so -t N means: at an FCD error, the contig is broken at the middle coordinate of the error, and then N bases get trimmed off each new contig end [0] ✂️✨

ngl the -a / -b situation is very much a pick-a-lane moment. you cannot have both. choose wisely bestie 🙈

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🌈 SEE ALSO 🌈

reapr(1) — go say hi to the parent 💜

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mwah, that's the whole page 🍓 this was REAPR-BREAK(1) from the REAPR manual, section 1 — kbye, go break something (an assembly, specifically) 💖✨🦋