Casava In Galaxy

Question: Casava In Galaxy

8.7 years ago by

Glen Otero • 30 wrote:

Hello- 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 greatly appreciated. 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? Thanks! Glen

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modified 8.7 years ago by Erick Antezana • 570 • written 8.7 years ago by Glen Otero • 30

8.7 years ago by

Erick Antezana • 570

Erick Antezana • 570 wrote:

Hi Glen, 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?). cheers, Erick

ADD COMMENT • link written 8.7 years ago by Erick Antezana • 570

Hi Erick- I'll try to keep the community posted on my progress, although that is likely to be unpredictable, just like my foreseeable development efforts. I'd like to hear from anyone that has incorporated a perl script into Galaxy and any advice they might have. Glen

ADD REPLY • link written 8.7 years ago by Glen Otero • 30

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 transcripts. 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 (http://www.fml.tuebingen.mpg.de/raetsch/lectures/NGS-Bioinformatics- Paris-Mar2010.pdf starting with slide 10) and the galaxy instance is available here http://galaxy.fml.mpg.de. 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. Cheers, Gunnar

ADD REPLY • link written 8.7 years ago by Gunnar Raetsch • 60

Glen, I forgot to mention an wiki page I came across last month (CASAVA is considered as a possible tool) : https://wiki.nbic.nl/index.php/Next_Generation_Sequencing:_Generic_pip eline cheers, Erick

ADD REPLY • link written 8.7 years ago by Erick Antezana • 570

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