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PROGRAM:

NAME

AmpliconNoise - remove noise from high throughput nucleotide sequence data

VERSION

This documentation refers to version 1.22

SYNOPSIS

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

DESCRIPTION

The following tools are included. Most of them have an MPI equivalent, for example
SeqNoise has an equivalent SeqNoiseM which can be used with mpirun.

FastaUnique - dereplicates fasta file
-in string input file name
Options:

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 - pairwise Needleman-Wunsch sequence distance matrix from a fasta file
-in string fata file name
Options:
-i output identifiers

Perseus - slays monsters
-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 from flowgrams
-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
-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
-in string fasta file name
Options:
-i output identifiers
-rin string lookup file name

SeqNoise - clusters sequences
-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
-din string dat filename
-min string map filename
-tin string tree filename
-s split size
-m min size

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