Registration request for Acyrthosiphon pisum NCBI assembly

[Scottyzy]

Hi, I'd like to have the genome for Acyrthosiphon pisum registered for the purpose of forging a BSgenome package. The assembly is pea_aphid_22Mar2018_4r6ur and below is the link to the NCBI page:

https://www.ncbi.nlm.nih.gov/assembly/GCF_005508785.1

Let me know if there's anything I can clear up or help with. Thank you very much.

[hpages]

Done in GenomeInfoDb 1.31.2 (see commit 513a854cb990dc6229f86af29f0fbc389bcb2a7f).

Note that whoever submitted the pea_aphid_22Mar2018_4r6ur assembly to NCBI messed it up:

• The name of the assembly is long and ugly.
• The reported assembly level should have been Scaffold, not Chromosome.
• The sequence names are terrible:

  library(GenomeInfoDb)
  Seqinfo(genome="pea_aphid_22Mar2018_4r6ur")
  # Seqinfo object with 21920 sequences (1 circular) from pea_aphid_22Mar2018_4r6ur genome:
  #   seqnames                    seqlengths isCircular                    genome
  #   Scaffold_21773;HRSCAF=24826  132544852      FALSE pea_aphid_22Mar2018_4r6ur
  #   Scaffold_20849;HRSCAF=22316  170740645      FALSE pea_aphid_22Mar2018_4r6ur
  #   Scaffold_21967;HRSCAF=25451  119541763      FALSE pea_aphid_22Mar2018_4r6ur
  #   Scaffold_21646;HRSCAF=24477   42333646      FALSE pea_aphid_22Mar2018_4r6ur
  #   MT                               16971       TRUE pea_aphid_22Mar2018_4r6ur
  #   ...                                ...        ...                       ...
  #   Scaffold_21962;HRSCAF=25426       1664      FALSE pea_aphid_22Mar2018_4r6ur
  #   Scaffold_21963;HRSCAF=25436       7008      FALSE pea_aphid_22Mar2018_4r6ur
  #   Scaffold_21964;HRSCAF=25444      82198      FALSE pea_aphid_22Mar2018_4r6ur
  #   Scaffold_21965;HRSCAF=25446      38071      FALSE pea_aphid_22Mar2018_4r6ur
  #   Scaffold_21966;HRSCAF=25449     558143      FALSE pea_aphid_22Mar2018_4r6ur

The Acyr_2.0 assembly from the Baylor College of Medicine seems cleaner (but is also a few years older). Also registered in GenomeInfoDb:

Seqinfo(genome="Acyr_2.0")
# Seqinfo object with 23925 sequences (1 circular) from Acyr_2.0 genome:
#   seqnames      seqlengths isCircular   genome
#   MT                 16971       TRUE Acyr_2.0
#   Scaffold1        2622152      FALSE Acyr_2.0
#   Scaffold2        2384549      FALSE Acyr_2.0
#   Scaffold3        1975979      FALSE Acyr_2.0
#   Scaffold4        2478080      FALSE Acyr_2.0
#   ...                  ...        ...      ...
#   Scaffold23920        605      FALSE Acyr_2.0
#   Scaffold23921        430      FALSE Acyr_2.0
#   Scaffold23922       1480      FALSE Acyr_2.0
#   Scaffold23923        812      FALSE Acyr_2.0
#   Scaffold23924        683      FALSE Acyr_2.0

H.

[Scottyzy]

Hi I was wondering how long before the assembly is available to use, as when i tried to run my seed files it said is not registered NCBI assembly. Thank you

[hpages]

Well, you need GenomeInfoDb 1.31.2. You can install it now (by installing it directly from GitHub) or wait that it becomes available in BioC 3.15 (this is BioC devel, it requires R 4.2), at which point you'll be able to install it via BiocManager::install(). This should take between 24h-48h.