Rob Davies - 2009-12-03

I have uploaded version 2.0.0 of the sequenceread package.  This includes a version of illumina2srf that can read intensity data in the .cif format that RTA produces.

You can download it from (https://sourceforge.net/projects/sequenceread/files/).  Here are the release notes:

Sequenceread package v2.0.0

This package includes illumina2srf which can be used to convert the
contents of an Illumina GA-pipeline run folder to the more convenient
SRF format.  Illumina2srf was originally part of the Staden io\_lib package
and was later shipped with the Illumina analysis software.  This version
is a major revision of the software which can support sequence bar codes
and more variants of the Illumina pipeline.  Also included is a helper
application called 'index\_decoder' which can be used to decode sequence
bar codes.

The most notable changes to illumina2srf are:

* Support for pipeline versions prior to 1.3 has been dropped.
* Support has been added for the RTA (real-time analysis) versions of the
   Illumina software.
* Illumina2srf now searches for the intensity files produced by all the
   different variants of the pipeline it supports automatically.  It should
   therefore no longer be necessary to use the -I flag for IPAR projects
   (although it shouldn't do any harm).
* When storing unprocessed data (using the -b or -r options) illumina2srf
   will no longer automatically include noise data (from *.nse.txt,
   *.nse.txt.p or *.cnf files).  If you do want to include this data, you will
   need to use the -nse option.
* Support has been added for samples that include sequence bar codes.  Such
   samples will first need to be processed using the included index\_decoder
   program to work out which bar code was attached to each sample and make
   a new set of .qseq.txt files.  These can then be processed by illumina2srf.
   You will need to use the new -use\_bases option to indicate which part
   of the read corresponds to the bar code tag.  This will change the REGN
   tag so that it indicates which bases comprise the bar code and will also
   make illumina2srf attach the name of the decoded tag to the end of the
   read name after a '#' character.  See the illumina2srf and index\_decoder
   man pages for more details.
* Some extra options have been added to give finer control over what
   data gets stored and which file variants are searched for.
* There is a new test harness to that does some basic checks to ensure that
   illumina2srf is storing the correct data.

Unlike previous versions of illumina2srf, this package does not come with a
version of io\_lib.  If you do not have it already, io_lib can be obtained
by downloading it from <https://sourceforge.net/projects/staden/files/> or
you may be able to install a pre-packaged version from your operating
system vendor.  You will need io\_lib version 1.12.1 or later.  When you
have installed io\_lib, you can build and install this package in the
standard GNU autoconf way by running 'configure' followed by 'make' and
'make install'.  Please see the INSTALL file for more details.