Feature Update: Expanded Reference Genomes for NGS Tools
Expanded genome data is now available on Galaxy's main server http://usegalaxy.org.
The expanded genome data are organized into the following categories:
Full = All chromosomes (or scaffolds/contigs) released as part of the full build from the data source. Many will also include the latest Mitochondrial chromosome, if available. Full is the default genome build type for all reference genomes and what was previously available.
Canonical = All chromosomes released that represent the core chromosomes (including mitochondrial) for that species and build. Canonical will not include chromosomes with names that include: chrUn, chrN_random, chrN_hap_XX (haplotype), and similar.
Coming soon will also be the reference genome variants Male and Female. Many genomes will default to Male (identical to Canonical). Female will be the Canonical minus a chrY chromosome.
The NGS Tools with expanded genome data available: Bowtie and BWA. Please note that previously used/saved settings will default to "Full". Other NGS Tools are planned to have expanded reference genome data available in the future as appropriate.
Reference genomes part of the expanded dataset include: galGal3 hg18 hg19 mm8 mm9 panTro2 rn4 taeGut1 tetNig1 tetNig2
Thanks for using Galaxy!
Galaxy team November 16, 2010