[galaxy-announce] Galaxy Main new native genomes & updated genomes

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[galaxy-announce] Galaxy Main new native genomes & updated genomes

Jennifer Jackson
Dear Galaxy Community,

Recent genome additions and updates on the Galaxy Main public instance at http://usegalaxy.org include:


New native genome additions:

  • "mm10": Mouse (Mus musculus) Dec 2011, GRCm38, source UCSC
  • "gorGor3": Gorilla (Gorilla gorilla gorilla) May 2011, WGS CABD02, source UCSC
  • "bosTau6": Cow (Bos taurus) Nov 2009, UMD_3.1, source UCSC

Existing genomes with content updates:

  • "bosTau4, bosTauMd3, canFam2, mm9, panTro3, rn4"

Details:

  • Native genomes are sometimes referred to as "locally cached" on tool forms.
  • New and updated indexes include:  NGS:+ (all tools), Lift-Over (Convert genome coordinates), and Fetch Sequences (Extract DNA).
  • Currently, these additions and updates exclude the tools in the group NGS: GATK Tools (beta), however new genomes will be added soon. For now, use the custom reference genome option with this tool group, if not using "Homo sapiens b37 (hg_g1k_v37)".
  • Additional new genomes and updates are in progress and will be announced via Twitter @galaxyproject and the galaxy-announce@... mailing list.
  • Genome requests can be sent to the [hidden email]mailing list. Please include the full genome name, a link to the stable public source, and any build or species specific information you feel is relevant. This helps us to create a reference genome the entire Galaxy community can use. 
  • Unfinished genomes or genomes not yet published to a stable source repository are still often best used as a custom reference genome with tools, but please feel free to check in for feedback.

Thanks for using Galaxy!

--
Jennifer Jackson
http://galaxyproject.org
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Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org