Provided by: ampliconnoise_1.29-7build1_amd64
AmpliconNoise - remove noise from high throughput nucleotide sequence data
This documentation refers to version 1.22
See /usr/share/doc/ampliconnoise/Doc.pdf.gz for details of how to run.
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
All software by Chris Quince (firstname.lastname@example.org) This manpage by Tim Booth (email@example.com)
LICENCE AND COPYRIGHT
Copyright (c) 2009 (firstname.lastname@example.org). 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.