The core facility that we use at UCLA for Illumina sequencing makes the read data available via rsync as qseq-formatted files. No demultiplexing is performed by the core facility. To make my life a little bit easier, and to help out my colleagues, I created a suite of tools that I call htSeqTools.
One tool handles the file transfer over rsync. A second tool uncompresses the qseq files if necessary, and then converts them to standard fastq format. The third demultiplexes them. The suite intelligently handles paired-end or single-end data. It is all designed to be simple to use, but with some extra features available when needed.
By default, the demultiplexer uses the standard set of 24 Illumina TruSeq indices. Alternatively, the user can specify the Nextera index sequences, or provide the provide the program with tab-delimited text file of any custom sequences. The user can specify that only perfect matches of the index sequence are allowed, or choose moderate or loose stringency matching.
The full suite is maintained in my bitbucket repository.
Sean Gallaher, PhD 