Suggestions reference genomes

[MonicaSolbakken]

May I suggest the following genomes which often are used as outgroups or as supplemental information in various biological analyses:

Genomes are available either at GenomeArk or ensembl.org

Model species:
Drosophila melanogaster
Mouse Mus musculus
Human Homo sapiens
Rat Rattus norvegicus
S. cerevisiae Saccharomyces cerevisiae
Zebrafish Danio rerio
Chicken Gallus gallus
Tropical clawed frog Xenopus tropicalis
C. elegans Caenorhabditis elegans

Evolutionary outgroups:
Coelacanth Latimeria chalumnae
Elephant shark Callorhinchus milii
Hagfish Eptatretus burgeri
Spotted gar Lepisosteus oculatus
Northern pike Esox lucius
Lamprey Petromyzon marinus
Atlantic cod Gadus morhua

Possible representatives for each of the major vertebrate lineages:
Lineage Species name Common name Order
Amphibian Bufo bufo common toad Anura
Amphibian Geotrypetes seraphini Gaboon caecilian Gymnophiona
Birds Aquila chrysaetos chrysaetos european golden eagle Accipitriformes
Birds Sterna hirundo common tern Charadriiformes
Cartilaginous Scyliorhinus canicula lesser-spotted catshark Carcharhiniformes
Cartilaginous Pristis pectinata smalltooth sawfish Pristiformes
Cartilaginous Amblyraja radiata Thorny skate Rajiformes
Fish Pygocentrus nattereri Red-bellied piranha Characiformes
Fish Antennarius maculatus warty frogfish Lophiiformes
Mammal Pipistrellus pipistrellus common popistrelle Chiroptera
Mammal Tachyglossus aculeatus short-beaked ehidna Monotremata
Mammal Sciurus carolinensis grey squirrel Rodentia
Reptile Thamnophis elegans Western terrestrial garter snake Squamata
Reptile Gopherus evgoodei Goode's thornscrub tortoise Testudines

All the best,
Monica Solbakken

[Sabryr]

Thank you for the information. This project is not just to mirror the genomes but to set it up in an a consistent way (with indices etc). We shall include those but I need some more details. I understand this will be too much work, but try to provide as much information you can if not all (you may ask your colleagues to contribute to this issue as well).

If you have access to saga can you please go to the following location (where we have started including references):

/cluster/shared/databases/references/
Then check if the genome you suggest is present. If yes, please check we have setup what you need.

If not, please check the example for Human:
/cluster/shared/databases/references/Homo_sapiens

For example
/cluster/shared/databases/references/Homo_sapiens/Ensembl
is what we have from Ensemble for human.

Then check the format and suggest what to include.
For example "Chicken Gallus gallus" find out how the genome is versioned and where the data can be downloaded and give the info here.