WTPOA-CNS(1)

💖 WTPOA-CNS(1) — the girlies' guide to wtpoa-cns 💖

okay so bestie, welcome to section 1 of the User Commands manual, and no cap, this is the wtpoa-cns page — the Consensuser for wtdbg using PO-MSA. Yes, it's giving very "I polish your contigs and I look cute doing it." Let's get into it. 🦋

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✨ NAME ✨

wtpoa-cns — Consensuser for wtdbg using PO-MSA

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✨ SYNOPSIS ✨

wtpoa-cns [options]

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✨ DESCRIPTION ✨

WTPOA-CNS: Consensuser for wtdbg using PO-MSA. That's the whole vibe, bestie. 💅

• Author: Jue Ruan <ruanjue@gmail.com>
• Version: 2.5 (20190621)

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✨ OPTIONS ✨

so there are a LOT of flags here and every single one of them matters, so let's go one by one, no skipping, fr fr:

• -t <int> — Number of threads. Default is [4]. Give her more threads, she'll go faster. 🏃♀️
• -d <string> — Reference sequences for SAM input. Using this will invoke sorted-SAM input mode. ✨
• -u <int> — XORed flags to handle SAM input. Default [0].
  • 0x1: Only process reference regions present in/between SAM alignments
  • 0x2: Don't fileter secondary/supplementary SAM records with flag (0x100 | 0x800)
• -r — Force to use reference mode.
• -p <string> — Similar with -d, but translate SAM into wtdbg layout file.
• -i <string> — Input file(s) *.ctg.lay from wtdbg, +, default [STDIN].

Or sorted SAM files when having -d/-p.

• -o <string> — Output files, default [STDOUT].
• -f — Force overwrite. (She's assertive. We love that. 👑)
• -j <int> — Expected max length of node, or say the overlap length of two adjacent units in layout file, default [1500]. bp overlap will be default to 1500 (or 150 for sam-sr) when having -d/-p, block size will be 2.5 * overlap.
• -b <int> — Bonus for tri-bases match, default [0].
• -M <int> — Match score, default [2].
• -X <int> — Mismatch score, default [-5].
• -I <int> — Insertion score, default [-2].
• -D <int> — Deletion score, default [-4].
• -H <float> — Homopolymer merge score used in dp-call-cns mode, default [-3].
• -B <expr> — Bandwidth in POA, [Wmin[,Wmax[,mat_rate]]], where mat_rate = matched_bases/total_bases, default [64,1024,0.92]. Program will double bandwidth from Wmin to Wmax when mat_rate is lower than setting.
• -W <int> — Window size in the middle of the first read for fast align remaining reads, default [200]. If $W is negative, will disable fast align, but use the abs($W) as Band align score cutoff.
• -w <int> — Min size of aligned size in window, default [$W * 0.5].
• -A — Abort TriPOA when any read cannot be fast aligned, then try POA.
• -S <int> — Shuffle mode:
  • 0: don't shuffle reads
  • 1: by shared kmers
  • 2: subsampling

Default [1].

• -R <int> — Realignment bandwidth, 0: disable, default [16].
• -c <int> — Consensus mode:
  • 0: run-length
  • 1: dp-call-cns

Default [0].

• -C <int> — Min count of bases to call a consensus base, default [3].
• -F <float> — Min frequency of non-gap bases to call a consensus base, default [0.5].
• -N <int> — Max number of reads in PO-MSA, default [20]. Keep in mind that I am not going to generate high accurate consensus sequences here. 😭
• -x <string> — Presets, default [].

sam-sr: polishs contigs from short reads mapping, accepts sorted SAM files

shorted for '-j 50 -W 0 -R 0 -b 1 -c 1 -N 50 -rS 2'

• -q — Quiet. 🤫
• -v — Verbose. 🗣️
• -V — Print version information and then exit.

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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. 🫶

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and that's the whole page bestie, periodt 💅✨ — this was wtpoa-cns version 2.5, dated April 2020, from the WTPOA-CNS(1) manual. go forth and consensus, ily 🎀🌸💖