WTDBG-CNS(1)

💖 WTDBG-CNS(1) — the group chat guide 💖

okay bestie, gather round — this is the user-commands manual page for wtdbg-cns, and yes it lives in section 1. It's the Consensuser for wtdbg, and I'm gonna walk you through every single flag like we're texting at 2am. No skipping, no "you get the gist". We do this properly. 💅

✨ NAME ✨

wtdbg-cns — the Consensuser for wtdbg. That's the whole vibe. 🦋

🌸 SYNOPSIS 🌸

wtdbg-cns [options]

Just the program and some options. She's lowkey simple like that. 🎀

💜 DESCRIPTION 💜

WTDBG-CNS: Consensuser for wtdbg ✨

• Author: Jue Ruan <ruanjue@gmail.com>
• Version: 1.1

That's it, that's the whole description. Short queen. 👑

🎀 OPTIONS 🎀

Every single one, in order, exactly as the original says. Let's go. 🫶

• -t <int> — Number of threads, [1]. Give her more threads, she goes faster. Periodt.
• -i <string> — Input file(s) *.utg.cns from wtdbg, +, [STDIN]. Yes bestie, that's a literal + in there, don't ask me, just write it down. Default is STDIN.
• -o <string> — Output files, [STDOUT]. Default is STDOUT. 🦋
• -f — Force overwrite. She will not ask twice. 💀
• -j <int> — Expected length of node, or, say it with me, the overlap length of two adject units in layout file, [1000] bp. (Yes the original says "adject", we keep it, character for character. 🙈)

───── BEG DBG options ─────

• -k <int> — Kmer size for long reads, [15].
• -Z <int> — Z-cutoff, drop the lower (score / <-X>), [4].
• -W <int> — W-cutoff, drop the lagger (position), [48]. In DAG correction, -W set the bandwidth of alignment. 🔥
• -H <int> — High coverage bonus, [1].
• -L <int> — High coverage cutoff = avg_cov / <-L>, [10].
• -c <int> — Candidate strategy, 0: best-kmers, 1: median length, 2: first (include), 3: first (exclude), 4: longest, 5, shortest, [0]. In DAG correction, force to use strategy 2. The way that one flag has SIX whole personalities 😭

───── END DBG options ─────

• -M <int> — Match score, [2].
• -X <int> — Mismatch score, [-7].
• -I <int> — Insertion score, [-3].
• -D <int> — Deletion score, [-4].
• -E <int> — Gap extension score, [-2].
• -m <int> — 1: DBG correction; 2: DAG correction, [1].
• -S <int> — whether to correct structure before error correction, [1].
• -v — Verbose. She tells you everything. 🍓
• -V — Print version information and then exit. Iconic exit, honestly. ✨

🌈 AUTHOR 🌈

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. 🫶 Giving credit where it's due, always.

and that's the whole page, bestie, we ate and left no crumbs 💅✨

This was wtdbg-cns 2.5, dated April 2020 — that's the source/version and the date, folded into a cute lil sign-off instead of a boring footer line. Bye bye, go run it. 👑🦋💖