Shalabh: To add to Jen's reply bowtie supports SOLiD csfasta and QUAL files natively. However, Galaxy has a tool for converting SOLiD output to fastq here: http://bit.ly/pXw3Ic Tx, anton galaxy team Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org On Aug 10, 2011, at 4:09 PM, Jennifer Jackson wrote:

Hello Shalabh,

Galaxy is open source and available here: http://bitbucket.org/galaxy/galaxy-central/src/

Check under tools to find: tools/fastq/fastq_groomer.py/.xml

Other SOLiD specific tools are under: tools/solid_tools/

The rest is organized in this same general way. This wiki may be helpful: http://galaxyproject.org/Admin/Tools/Tool%20Config%20Syntax

Hopefully this helps. Next time, you can just send to one list, and for development questions, the best list would be galaxy-dev@bx.psu.edu. http://galaxyproject.org/Support

Best,

Jen Galaxy team

On 8/10/11 11:23 AM, Shalabh Sharma wrote:

...

Hi, I am trying to implement a SOLID pipeline for my solid data. I really like the pipeline used in Galaxy, I was looking for conversion of SOLID to fastq, but it didn't say that how it is achieved in Galaxy. I know for bwa you can use solid2fasta.pl but for bowtie i did not find any program or information. I would really appreciate if you can help me with this, like how it is achieved and where i can download the program used by Galaxy.

Thanks Shalabh Sharma -----------------------------

Shalabh Sharma Scientific Computing Professional Associate (Bioinformatics Specialist) Department of Marine Sciences University of Georgia Athens, GA 30602-3636

___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists, please use the interface at:

http://lists.bx.psu.edu/

-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists, please use the interface at:

http://lists.bx.psu.edu/