inst/registered/NCBI_assemblies/Canis_lupus_familiaris.R

In GenomeInfoDb: Utilities for manipulating chromosome names, including modifying them to follow a particular naming style

ORGANISM <- "Canis lupus familiaris"

### List of assemblies first by breed then by date.
### Yep, different genome assemblies can have the same name! (don't ask me why)
### Lookup by genome name will pick-up the first in the list.
ASSEMBLIES <- list(
    ## breed: boxer
    list(assembly="CanFam2.0",
         date="2005/07/12",
         extra_info=c(breed="boxer"),
         assembly_accession="GCF_000002285.1",
         circ_seqs=character(0)),

    list(assembly="CanFam2.0",
         date="2005/07/12",
         extra_info=c(breed="boxer"),
         assembly_accession="GCF_000002285.2",  # canFam2
         circ_seqs="MT"),

    list(assembly="CanFam3.1",
         date="2011/11/02",
         extra_info=c(breed="boxer"),
         assembly_accession="GCF_000002285.3",  # canFam3
         circ_seqs="MT"),

    list(assembly="UU_Cfam_GSD_1.0",
         date="2020/03/10",
         extra_info=c(breed="German Shepherd"),
         assembly_accession="GCA_011100685.1",  # canFam4
         circ_seqs="chrM")
)