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

AUTHOR

       All software by Chris Quince (quince@civil.gla.ac.uk) This manpage by Tim Booth
       (tbooth@ceh.ac.uk)

LICENCE AND COPYRIGHT

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

       Released under the Lesser GPL.

       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.