SYNOPSIS

ayb [-c coordinate_file] [-d prefix] [-f format] [-i iterations] [-l lane] [-L minlam] [-m mu] [-n machine_name] [-o outfile] [-r run_number] [-s threshold] [-t tile] -z data.cif

ayb --help

ayb --licence

DESCRIPTION

AYB is an advanced basecaller for the Illumina sequencing platform, producing basecalls and associated quality measures from raw intensity information (CIF format files).

AYB reads intensity data from the file given on the commandline, or from stdin if no file is given, and writes the results to stdout unless an alternative -o outfile is specified. Messages, errors and progress indications are written to stderr.

-c, --coordinates file [default: none]

File to read coordinates of clusters. Required for qseq output.

-d, --dump prefix [default: don’t dump]

Dump information about run parameters.

-f, --format format [default: fastq]

Format to output results in. Choices are fasta, fastq and qseq.

-i, --iterations niterations [default: 5]

Number of iterations of refinement to use.

-l, --lane lane [default: 0]

Lane number for output.

-L, --lambda lambda [default: 0]

Minimum allowed lambda.

-m, --mu value [default: 1e-5]

Mu for quality adjustment.

-n, --name machine_name [default: unknown]

Name of machine for qseq output.

-o, --outfile outfile [default: stdout]

File to write output to.

-r, --run run_number [default: 0]

Run number for qseq output.

-s , --spike threshold [default: don’t remove]

Move spikes by zeroing intensities. If any base in a cycle for a given cluster is greater than threshold then set all intensities to zero.

-t, --tile tile [default: 0]

Tile number for output.

-z, --zero

Set negative observed intensities to zero.

-h, --help

Display information about usage and exit.

--licence

Display licence terms and exit.

EXAMPLE

ayb s_4_0033.cif > s_4_0033.fastq

AUTHOR

Written by Tim Massingham, tim.massingham@ebi.ac.uk

Contains the Non-Negative Least Squares routine of Charles L. Lawson and Richard J. Hanson (Jet Propulsion Laboratory, 1973). See http://www.netlib.org/lawson-hanson/ for details.

RESOURCES

See http://www.ebi.ac.uk/goldman/AYB/.

COPYING

Copyright © 2010 European Bioinformatics Institute. Free use of this software is granted under the terms of the GNU General Public License (GPL). See the file COPYING in the ciftools distribution or http://www.gnu.org/licenses/gpl.html for details.

SEE ALSO

ciftools(1)