REAPR(1)

💅 REAPR — the manual page, but make it cute

okay so bestie, you opened REAPR(1) — yes that's the manual section 1 header, we're in the big leagues now ✨ — and lemme tell you, reapr is the moment.

✨ NAME ✨

reapr — the universal tool for genome assembly evaluation 🧬👑

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🌸 SYNOPSIS 🌸

reapr <task> [options]

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🦋 DESCRIPTION 🦋

reapr is the main executable for the REAPR software. But here's the tea: the actual functionality isn't living in reapr itself — it's all handed off to the subtools, aka the tasks. So reapr is like the group chat admin who doesn't do the work but organizes everyone who does. 🫶

🎀 Common tasks

• facheck — checks IDs in fasta file. just. checks them. it's giving quality control 💅
• smaltmap — map read pairs using SMALT: makes a BAM file to be used as input to the pipeline 🔥
• perfectmap — make perfect uniquely mapping plot files ✨
• pipeline — runs the REAPR pipeline, using an assembly and mapped reads as input, and optionally results of perfectmap. (It runs facheck, preprocess, stats, fcdrate, score, summary and break) — yeah it's the whole main character energy run 🏃♀️
• plots — makes Artemis plot files for a given contig, using results from stats (and optionally results from score) 📈
• seqrename — renames all sequences in a BAM file: use this if you already mapped your reads but then found facheck failed — saves remapping the reads so that pipeline can be run 😭🙏 (literally the "bestie I already walked to the store" of subtools)

💜 Advanced tasks

• preprocess — preprocess files: necessary for running stats 🧚
• stats — generates stats from a BAM file 📊
• fcdrate — estimates FCD cutoff for score, using results from stats 🎯
• score — calculates scores and assembly errors, using results from stats ⭐
• summary — make summary stats file, using results from score 📝
• break — makes broken assembly, using results from score 💔 (yes, broken. on purpose. it's fine.)
• gapresize — experimental, calculates gap sizes based on read mapping ⚠️ (experimental, so vibe check accordingly)
• perfectfrombam — generate perfect mapping plots from a bam file (alternative to using perfectmap for large genomes) 🐘

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🌈 SEE ALSO 🌈

all the sibling pages, go give them a follow, they're iconic:

reapr-facheck(1), reapr-smaltmap(1), reapr-perfectmap(1), reapr-pipeline(1), reapr-plots(1), reapr-seqrename(1), reapr-preprocess(1), reapr-stats(1), reapr-fcdrate(1), reapr-score(1), reapr-summary(1), reapr-break(1), reapr-gapresize(1), reapr-perfectfrombam(1) 💖

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and that's the whole page bestie — signed off at the very bottom with REAPR(1), manual section 1, date and all, no cap 🎀✨