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@bx.psu.edu mailing list.
• Genome requests can be sent to the mailto:galaxy-user@bx.psu.edu 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