Hi Glen & Erick,
FYI, we have a pipeline running on our site, which works for Illumina reads (starting with
FASTQ files) and covers some parts of the described pipeline. It allows you to align reads
with a few read mappers, to quantitate transcripts, and also to predict novel
Some of these tools are not fully integrated into galaxy yet, but others should be fully
functional. We are currently work on improving their interaction and to get bugs fixed.
The underlying methods are described in the slides of a recent talk
starting with slide 10) and the galaxy instance is available here
Some of the tools have not been released/published yet, but will be hopefully soon.
In this case we will also provide the galaxy bindings.
> I am very interested in such a development. AFAIK, there
isn't (yet) a
> Galaxy tool(s) that such pipeline. I am pretty sure this will be of
> great interest within the NGS/Galaxy community. Please keep us updated
> about its progress (maybe via the bitbucket wiki?).
> On 30 March 2010 09:30, Glen Otero <gotero(a)linuxprophet.com> wrote:
>> I'm about to embark on an effort to try and roll Illumina's CASAVA
pipeline software--demultiplex.pl, GERALD.pl, run.pl and other scripts, into a local
Galaxy install. I'd prefer not to reinvent the wheel, so I'd like to hear from
anyone that's already done part or all of what I'm going to attempt. Any advice is
>> Alternatively, if this is something that other developers are interested in,
maybe it could be considered for a coding sprint during the breakout session at the
developers' conference or during one of the BEER sessions?
>> galaxy-user mailing list
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