Question: New Builds And Associated Genome Data
0
Kelly Vincent • 340 wrote:
Hi everyone,
Over the last few weeks, quite a bit of genome data has been added to
Galaxy. This includes some completely new builds, generally with NGS
and LiftOver when possible. Several genomes (old and new) now have the
concept of full, canonical and other possible variants. There are also
more LiftOver files for all of the current builds, when available.
Additionally, NGS indexes have been prepared for several existing
builds. The relevant genomes for each category are listed below
(including the database name used in Galaxy).
We are always willing to consider adding new genomes, so if you know
of one that would be beneficial to at least several people, email us
with links to the definitive (fasta or 2bit) source file(s) and we
will consider adding it (but there are no promises).
The wiki page https://bitbucket.org/galaxy/galaxy-
central/wiki/GenomeData
also describes our genome data.
Regards,
Kelly
===================================================
BRAND NEW DATA
- Aedes aegypti: AaegL1
- Anopheles gambiae: AgamP3
- Armadillo: dasNov1
- C. brenneri: caePb1, caePb2
- C. briggsae: cb3
- C. intestinalis: ci2
- C. japonica: caeJap1
- C. remanei: caeRem3
- Cat: felCat4
- Cow: bosTauMd3 and bosTau5 (liftOver only for both)
- Culex quinquefasciatus: CpipJ1
- Elephant: loxAfr3
- Fission Yeast: Schizosaccharomyces_pombe_1.1
- Fruit Fly: droWil1
- Ixodes scapularis: IscaW1
- J. Craig Venter: venter1
- Lancelet: braFlo1
- Mouse-ear Cress: Arabidopsis_thaliana_TAIR9
- P. pacificus: priPac1
- Pediculus humanus: PhumU1
- pUC18
- Rabbit: oryCun2
- Rice: oryza_sativa_japonica_nipponbare_IRGSP4.0
- Sea Hare: aplCal1
- T. castaneum: triCas2
- Tetraodon: tetNig2
GENOMES WITH VARIANTS
- Full (every contig etc. that is available) and Canonical (named
chromosomes only)
+ calJac3
+ cb3
+ ci2
+ felCat4
+ galGal3
+ hg18 and hg19
+ mm8 and mm9
+ oryLat2
+ panTro2
+ rn3 and rn4
+ taeGut1
+ tetNig1 and tetNig2
- Female (Same as Canonical without Y chromosome)
+ mm9
GENOMES NOW WITH NGS DATA
- Enterobacter sp. 638: ente638
- Marmoset: calJac3
- Panda: ailMel1
- Rabbit: oryCun2
- E. coli APEC O1: eschColi_APEC_O1
- E. coli CFT073: eschColi_CFT073
- E. coli K12 strains
+ DH10B: eschColi_K12_DH10B
+ MG1655: eschColi_K12_MG1655
+ W3110: eschColi_K12_W3110
- E. coli O157H7 strains:
+ EC4115: eschColi_O157H7_EC4115
+ EDL933: eschColi_O157H7_EDL933
+ Sakai: eschColi_O157H7
+ TW14359: eschColi_O157H7_TW14359
- Burkholderia pseudomallei 668: 13953
- Burkholderia pseudomallei 1106a: burkPseu_1106A
- Burkholderia pseudomallei 1710b: 13954
- Burkholderia pseudomallei K96243: 178