where to get indexes for mapping tools
Hi, we have set up a Galaxy server for internal use. We would like to provide indexes for NGS mapping tools for a set of organisms that are relevant to our research. While bowtie has a repository of such indexes, other tools, e.g. bwa, don't seem to have one, so we have to build our own. Is there a repository of pre-built indexes for all mapping tools supported by Galaxy somewhere? Thanks. Yury -- Yury V. Bukhman, Ph.D. Associate Scientist, Bioinformatics Great Lakes Bioenergy Research Center University of Wisconsin - Madison 445 Henry Mall, Rm. 513 Madison, WI 53706, USA Phone: 608-890-2680 Fax: 608-890-2427 Email: ybukhman@glbrc.wisc.edu
Yury Bukhman wrote:
Hi,
we have set up a Galaxy server for internal use. We would like to provide indexes for NGS mapping tools for a set of organisms that are relevant to our research. While bowtie has a repository of such indexes, other tools, e.g. bwa, don't seem to have one, so we have to build our own. Is there a repository of pre-built indexes for all mapping tools supported by Galaxy somewhere?
Hi Yury, We are working on setting up a mirror of all of our reference data that will be accessible via rsync and possibly http. There'll be an announcement when this is available. --nate
Thanks.
Yury
-- Yury V. Bukhman, Ph.D. Associate Scientist, Bioinformatics Great Lakes Bioenergy Research Center University of Wisconsin - Madison 445 Henry Mall, Rm. 513 Madison, WI 53706, USA Phone: 608-890-2680 Fax: 608-890-2427 Email: ybukhman@glbrc.wisc.edu
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Thanks, Nate! I think this would be a very useful resource. Yury On 04/04/11, Nate Coraor wrote:
Yury Bukhman wrote:
Hi,
we have set up a Galaxy server for internal use. We would like to provide indexes for NGS mapping tools for a set of organisms that are relevant to our research. While bowtie has a repository of such indexes, other tools, e.g. bwa, don't seem to have one, so we have to build our own. Is there a repository of pre-built indexes for all mapping tools supported by Galaxy somewhere?
Hi Yury,
We are working on setting up a mirror of all of our reference data that will be accessible via rsync and possibly http. There'll be an announcement when this is available.
--nate
Thanks.
Yury
-- Yury V. Bukhman, Ph.D. Associate Scientist, Bioinformatics Great Lakes Bioenergy Research Center University of Wisconsin - Madison 445 Henry Mall, Rm. 513 Madison, WI 53706, USA Phone: 608-890-2680 Fax: 608-890-2427 Email: ybukhman@glbrc.wisc.edu
___________________________________________________________ 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:
-- Yury V. Bukhman, Ph.D. Associate Scientist, Bioinformatics Great Lakes Bioenergy Research Center University of Wisconsin - Madison 445 Henry Mall, Rm. 513 Madison, WI 53706, USA Phone: 608-890-2680 Fax: 608-890-2427 Email: ybukhman@glbrc.wisc.edu
participants (2)
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Nate Coraor -
Yury Bukhman