ORGANISM <- "Gallus gallus"
### List of assemblies 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(
## 17152 sequences.
list(assembly="Gallus_gallus-2.1",
date="2006/11/01",
assembly_accession="GCF_000002315.2", # galGal3
circ_seqs="MT"),
## 17151 sequences, same as in the GCF_000002315.2 assembly above except
## that MT is missing.
## Also note that the 17151 sequences in GCF_000002315.1 are the same as
## in GCA_000002315.1 but 14 of them have different GenBank accessions.
list(assembly="Gallus_gallus-2.1",
date="2006/11/01",
assembly_accession="GCF_000002315.1",
circ_seqs=character(0)),
list(assembly="Gallus_gallus-4.0",
date="2011/11/22",
assembly_accession="GCA_000002315.2", # galGal4
circ_seqs="MT"),
list(assembly="Gallus_gallus-5.0",
date="2015/12/16",
assembly_accession="GCF_000002315.4", # galGal5
circ_seqs="MT"),
list(assembly="Ogye1.0",
date="2017/12/05",
assembly_accession="GCA_002798355.1",
circ_seqs="Ogye_chrM"),
list(assembly="GRCg6",
date="2018/02/02",
assembly_accession="GCA_000002315.4",
circ_seqs=character(0)),
## 464 sequences, same as in GCF_000002315.5.
## MT is NC_001323.1 (16775 bp), but this RefSeq record got removed
## by RefSeq stack, don't know why!
list(assembly="GRCg6a",
date="2018/03/27",
assembly_accession="GCA_000002315.5", # galGal6
circ_seqs="MT"),
## 464 sequences, same as in the GCA_000002315.5/GCF_000002315.5 assembly
## above except that MT now is NC_040902.1 (16784 bp).
list(assembly="GRCg6a",
date="2018/03/27",
assembly_accession="GCF_000002315.6",
circ_seqs="MT"),
## 214 sequences, same as in GCA_016699485.1.
list(assembly="bGalGal1.mat.broiler.GRCg7b",
date="2021/01/19",
assembly_accession="GCF_016699485.2",
circ_seqs="MT"),
## 276 sequences.
list(assembly="bGalGal1.pat.whiteleghornlayer.GRCg7w",
date="2021/10/01",
assembly_accession="GCA_016700215.2",
circ_seqs=character(0)),
## 255 sequences, same as in GCA_016700215.1.
## Make sure to keep **after** the GCA_016700215.2 assembly above which
## has the same name but is more recent.
list(assembly="bGalGal1.pat.whiteleghornlayer.GRCg7w",
date="2021/01/19",
assembly_accession="GCF_016700215.1",
circ_seqs=character(0))
)
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