RACON(1)

🌸 RACON(1) 🌸

okay bestie, welcome to racon — the consensus module for raw de novo DNA assembly of long uncorrected reads. yes it's a mouthful, no I will not be shortening it. this is the RACON(1) page from the User Commands corner of your manual, and I'm about to make it make sense 💖

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✨ NAME ✨

racon — consensus module for raw de novo DNA assembly of long uncorrected reads 🧬

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✨ SYNOPSIS ✨

(and yes the original page spells it SYNPOPSIS, iconic typo, we respect it 🎀)

racon [options ...] <sequences> <overlaps> <target sequences>

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✨ DESCRIPTION ✨

So here's the whole vibe. Racon is meant to be a standalone consensus module — like, it shows up on its own, no entourage — and its whole job is correcting raw contigs that came out of rapid assembly methods that skipped the consensus step entirely 🙈. The goal? Generate genomic consensus that's similar or better quality compared to what you'd get from assembly methods that do both error correction and consensus, while being several times faster than those methods. And it plays nice with data from both Pacific Biosciences and Oxford Nanopore Technologies. bestie it's giving versatile 💅

You can also use Racon as a polishing tool after assembly — either with Illumina data or with data from third generation sequencing. And the type of data you feed it? automatically detected. no cap, you don't have to tell it anything ✨

Racon takes exactly three input files, that's it, no more no less:

• contigs in FASTA/FASTQ format
• reads in FASTA/FASTQ format
• overlaps/alignments between the reads and the contigs in MHAP/PAF/SAM format

Output is a set of polished contigs in FASTA format, printed straight to stdout. And listen — all of those input files can be compressed with gzip. slay 🫶

Racon can also do a whole other thing: read error-correction. In that scenario the MHAP/PAF/SAM file needs to contain pairwise overlaps between reads, including dual overlaps. don't skip that part, it matters 💀

There's also a wrapper script available to make life easier for the end-user with large datasets. Same interface as racon, but it adds two extra features from the outside:

• Sequences can be subsampled to decrease the total execution time — accuracy might be lower though, lowkey a tradeoff 😭
• Target sequences can be split into smaller chunks and run sequentially to decrease memory consumption

And yes, both of those features can run at the same time. multitasking queen 👑

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✨ OPTIONS ✨

🌈 the three inputs (yes they're options, no I don't make the rules)

• <sequences> — input file in FASTA/FASTQ format (can be compressed with gzip) containing the sequences used for correction 🧬
• <overlaps> — input file in MHAP/PAF/SAM format (can be compressed with gzip) containing overlaps between sequences and target sequences 🔗
• <target sequences> — input file in FASTA/FASTQ format (can be compressed with gzip) containing the sequences which will be corrected ✨

🎀 optional 🎀

• -u, --include-unpolished — output unpolished target sequences. like, the raw ones, untouched 💅
• -f, --fragment-correction — perform fragment correction instead of contig polishing. heads up bestie: the overlaps file should contain dual/self overlaps! ⚠️
• -w, --window-length <int> — default: 500. the size of the window on which POA is performed 🪟
• -q, --quality-threshold <float> — default: 10.0. threshold for average base quality of the windows used in POA ⭐
• -e, --error-threshold <float> — default: 0.3. maximum allowed error rate used for filtering overlaps 🚫
• -m, --match <int> — default: 5. score for matching bases ✅
• -x, --mismatch <int> — default: -4. score for mismatching bases ❌
• -g, --gap <int> — default: -8. gap penalty — and it must be negative, don't fight it 🕳️
• -t, --threads <int> — default: 1. number of threads 🧵
• --version — prints the version number 📌
• -h, --help — prints the usage 🆘

ok real talk, those defaults are the defaults, don't come for me, I'm just the messenger 🫶

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✨ AUTHOR ✨

This manpage was written by Andreas Tille for the Debian distribution, and can be used for any other usage of the program. thank you Andreas, you ate 💖

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and that's the whole page bestie!! this was racon version 1.3.1, dated June 2018, living under RACON(1) — go polish something gorgeous 🌸✨🦋