AMPLICONNOISE(1)

💖 AMPLICONNOISE 💖

okay bestie, so this page is AmpliconNoise — it removes noise from high throughput nucleotide sequence data ✨ and honestly? iconic behaviour.

🌸 VERSION 🌸

bestie this doc is serving version 1.22 and yes we're keeping receipts 💅

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🦋 SYNOPSIS 🦋

so like... the actual how-to-run instructions are not in here, they're in:

See /usr/share/doc/ampliconnoise/Doc.pdf.gz for details of how to run.

go read the PDF, it's giving textbook energy 📖

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✨ DESCRIPTION ✨

okay so here's the whole squad. these are the tools included, and most of them have an MPI equivalent — like for example SeqNoise has an equivalent called SeqNoiseM which you can run with mpirun. parallel girlies rise 🫶

💅 FastaUnique

dereplicates a fasta file. that's the whole vibe.

FastaUnique -in string   input file name

Options: (that's it, she's lowkey minimal 💀)

🎀 FCluster

FCluster
  -in    string            distance input file name
  -out   string            output file stub

Options:

• -r — resolution
• -a — average linkage
• -w — use weights
• -i — read identifiers
• -s — scale dist.

🧚 NDist

gives you a pairwise Needleman-Wunsch sequence distance matrix, straight from a fasta file 👑

NDist -in string   fata file name

(yes, "fata" — the original says fata, we don't rewrite the lore, we respect it 🙈)

Options:

• -i — output identifiers

🔥 Perseus

slays monsters. not kidding, that's literally what the doc says and honestly? main character energy 👑

Perseus -sin string   seq file name

Options:

• -tin string — reference sequence file
• -a — output alignments
• -d — use imbalance
• -rin string — lookup file name

🦋 PyroDist

pairwise distance matrix, but make it flowgrams 💫

PyroDist
  -in    string            flow file name
  -out   stub              out file stub

Options:

• -ni — no index in dat file
• -rin string — lookup file name

💜 PyroNoise

clusters flowgrams without alignments — no cap, she does it alignment-free

PyroNoise
  -din   string            flow file name
  -out   string            cluster input file name
  -lin   string            list file

Options:

• -v — verbose
• -c double — initial cut-off
• -ni — no index in dat file
• -s double — precision
• -rin file — lookup file name

⭐ SeqDist

pairwise distance matrix from a fasta file, the sequel 🍓

SeqDist
  -in    string            fasta file name

Options:

• -i — output identifiers
• -rin string — lookup file name

🌈 SeqNoise

clusters sequences, she's the moment, she's the blueprint ✨

SeqNoise
  -in      string            sequence file name
  -din     string            distance matrix file name
  -out     string            cluster input file name
  -lin     string            list file

Options:

• -min — mapping file
• -v — verbose
• -c double — initial cut-off
• -s double — precision
• -rin string — lookup file name

💖 SplitClusterEven

SplitClusterEven
  -din    string  dat filename
  -min    string  map filename
  -tin    string  tree filename
  -s      split size
  -m      min   size

split evenly, live evenly, periodt 💅

🌸 pssst — every one of these tools keeps its exact flags, args and file stubs the way they are. don't rename anything, don't "fix" anything, just vibe and run it correctly iykyk

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👑 AUTHOR 👑

all the software is by Chris Quince (quince@civil.gla.ac.uk) 💜

and this manpage? by Tim Booth (tbooth@ceh.ac.uk) 🫶

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📜 LICENCE AND COPYRIGHT 📜

Copyright (c) 2009 (quince@civil.gla.ac.uk). All rights reserved.

released under the Lesser GPL 💅

and like, permission is granted for anyone to copy, use, or modify these programs and documents for purposes of research or education — provided this copyright notice is retained, and note is made of any changes that have been made. so keep the receipt bestie 🧾✨

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okay that's the whole page, she's from somewhere around perl v5.40.1, dated 2025-11-17, and she's filed under AMPLICONNOISE(1) — love that for her 💖🌈🦋 go forth and denoise, queen 👑