Add Other Genomes To Galaxy

7.9 years ago by

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello Xintao, We are happy to add new genomes. Would you be able to confirm that this is the correct source at NCBI? Project ID: 11756? Not all chromosomes are completely assembled for this project and there are two projects for the genome. http://www.ncbi.nlm.nih.gov/genomeprj?term=Trypanosome%20brucei%20927 If there is another source (Sanger appear to also have this genome as an ongoing working project), a pointer would be helpful. Completed genomes from stable sources with named and dated releases are preferred. If there is a common name used by the T. brucei 927 community for research that you want to share, we could include that in our documentation/genome naming. Meanwhile, you can always upload the genome yourself and use it with most tools from your history. The new FTP upload feature would be the recommended loading tool. We look forward to your reply, Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org

ADD COMMENT • link written 7.9 years ago by Jennifer Hillman Jackson ♦ 25k

7.9 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello Rob, We will add this to our to-do list for new genomes. Thanks for sending the Genbank information! Next time, if you could send requests to galaxy-user, that would be very helpful for the team. Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org

ADD COMMENT • link written 7.9 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen et al., Sorry to be a pest, but do you have an estimate for when the Hydra genome will be added to Galaxy? Cheers, Rob Rob Steele, Ph.D. Professor D240 Medical Sciences I Department of Biological Chemistry School of Medicine University of California, Irvine Irvine, CA 92697-1700 phone: 949-824-7341 e-mail: resteele@uci.edu fax: 949-824-2688 web: http://polyp.biochem.uci.edu/wiki/index.php/Main_Page

ADD REPLY • link written 7.8 years ago by Rob Steele • 40

Hello Rob, This genome is being worked on right now and should be available soon. Please feel free to check back a few weeks again for an update if you do not see it by then. Thanks! Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

ADD REPLY • link written 7.8 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen, How are things progressing with the Hydra genome? Cheers, Rob Rob Steele, Ph.D. Professor D240 Medical Sciences I Department of Biological Chemistry School of Medicine University of California, Irvine Irvine, CA 92697-1700 phone: 949-824-7341 e-mail: resteele@uci.edu fax: 949-824-2688 web: http://polyp.biochem.uci.edu/wiki/index.php/Main_Page

ADD REPLY • link written 7.7 years ago by Rob Steele • 40

Hi Rob, The project ABRM00000000 links to several thousand individual WGS submissions. Are there scaffolds or some type of assembled sequence available? Or, perhaps there an alternate source? Also, did you want us to include the two mitochondrial genomes from NCBI in the main assembly (once we have it?). This is common for us to do, but not required. And finally, if there is a short-hand name for the genome that you and the Hydra community use, we can assign that as the short-label for the genome. Otherwise, we just use the Genus_species_source_date for the label. Some way to distinguish from ACZU00000000 seems important. Thanks Rob, we look forward to your feedback. Jen -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

ADD REPLY • link written 7.7 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen, The easiest way to refer to this genome would be Hydra_JCVI. This way we know it is the JCVI assembly (ABRM00000000). ACZU00000000 is a separate assembly that was done at Berkeley. Including the two mitochondrial genomes would be a good idea. The many WGS submissions under ABRM00000000 are the scaffolds/contigs from the JCVI assembly. Because we were unable to obtain long-insert clones (e.g. BACs), the assembly is more fragmented than is typical for a metazoan genome assembly, and thus it has more scaffolds/contigs than is typical. Cheers, Rob Rob Steele, Ph.D. Professor D240 Medical Sciences I Department of Biological Chemistry School of Medicine University of California, Irvine Irvine, CA 92697-1700 phone: 949-824-7341 e-mail: resteele@uci.edu fax: 949-824-2688 web: http://polyp.biochem.uci.edu/wiki/index.php/Main_Page

ADD REPLY • link written 7.7 years ago by Rob Steele • 40

Thanks Rob, This definitely helps - we appreciate the additional info. This is on our high-priority list and Kelly will get back to you if we have more questions. Best, Jen -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

ADD REPLY • link written 7.7 years ago by Jennifer Hillman Jackson ♦ 25k

Hi, Hydra_JCVI is now available in Galaxy for several tools, including NGS analysis. Let us know if you run into any problems using it. Regards, Kelly

ADD REPLY • link written 7.7 years ago by Kelly Vincent • 340

Hi Kelly, Thanks much! Cheers, Rob Rob Steele, Ph.D. Professor D240 Medical Sciences I Department of Biological Chemistry School of Medicine University of California, Irvine Irvine, CA 92697-1700 phone: 949-824-7341 e-mail: resteele@uci.edu fax: 949-824-2688 web: http://polyp.biochem.uci.edu/wiki/index.php/Main_Page

ADD REPLY • link written 7.7 years ago by Rob Steele • 40

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