NCBI’s Reference Sequence (RefSeq) FTP release numbers will increment to 200 for the next release and skip over the numbers 100-199. The current, March 2020 release, is release 99. The next bi-monthly release in May 2020 will be release 200. This change is to avoid overlapping with the release numbers of the completely independent RefSeq annotation releases for the eukaryotic genomes we annotate, which are currently in the range 100-109, for example Mus musculus Annotation Release 108. Continue reading “The next RefSeq FTP release number will skip to 200”
Tag: Eukaryotic genome annotation
Fifteen new NCBI annotations in RefSeq: flies, harbor seal and more
In January and February, the NCBI Eukaryotic Genome Annotation Pipeline released new annotations in RefSeq for the following organisms:
- Aythya fuligula (tufted duck)
- Camelus ferus (Wild Bactrian camel)
- Corvus moneduloides (New Caledonian crow)
- Coturnix japonica (Japanese quail)
- Drosophila ananassae (fly)
- Drosophila virilis (fly)
- Etheostoma spectabile (orangethroat darter)
- Hylobates moloch (silvery gibbon)
- Mustela erminea (ermine)
- Nematostella vectensis (starlet sea anemone)
- Nomia melanderi (Alkali bee)
- Phoca vitulina (harbor seal)
- Sapajus apella (Tufted capuchin)
- Thamnophis elegans (Western terrestrial garter snake)
- Xiphophorus hellerii (green swordtail)
See more details on the Eukaryotic RefSeq Genome Annotation Status page.
Important changes to the genomes FTP site in February
We have added the latest NCBI Eukaryotic Genome Annotation Pipeline results for the more than 580 species that we annotate to the genomes/refseq directory on the genomes FTP area. As we announced in December, we will stop publishing annotation results to the genus_species directories (example: genomes/Xenopus_tropicalis) on the genomes FTP site effective February 1, 2020. We will also move existing genus_species directories to genomes/archive/old_refseq during the month of February.
Figure 1. The Assembly page for the Xenopus tropicalis UCB Xtro 10.0 (GCF_000004195.4) showing the blue download button. Annotation results such as the RefSeq transcript alignments that can be downloaded from the web page are now also under the genomes/refseq directory on the FTP site. The FTP path to the .bam alignment files is in red.
These FTP changes do not affect the Assembly download function. As always, you can download assembly data using the blue Download button on the web pages (Figure 1).
December 2019 RefSeq annotations: human, Tasmanian devil and more
In December, the NCBI Eukaryotic Genome Annotation Pipeline released new annotations in RefSeq for the following organisms:
- Anarrhichthys ocellatus (wolf-eel)
- Apis florea (little honeybee)
- Contarinia nasturtii (swede midge)
- Cucumis sativus (cucumber)
- Galleria mellonella (greater wax moth)
- Homo sapiens (human)
- Nasonia vitripennis (jewel wasp)
- Oncorhynchus kisutch (coho salmon)
- Oreochromis aureus (blue tilapia)
- Piliocolobus tephrosceles (Ugandan red Colobus)
- Sarcophilus harrisii (Tasmanian devil)
- Xenopus tropicalis (tropical clawed frog)
See more details on the Eukaryotic RefSeq Genome Annotation Status page.
November 2019 RefSeq annotations: honeybee, turkey and more
In November, the NCBI Eukaryotic Genome Annotation Pipeline has released new annotations in RefSeq for the following organisms:
Continue reading “November 2019 RefSeq annotations: honeybee, turkey and more”
August-October 2019 RefSeq annotations: mouse, firefly and more
Recently, the NCBI Eukaryotic Genome Annotation Pipeline has released new annotations in RefSeq for the following organisms:
- Aedes albopictus (Asian tiger mosquito)
- Aquila chrysaetos chrysaetos (golden eagle)
- Archocentrus centrarchus (flier cichlid)
- Calypte anna (Anna’s hummingbird)
- Camarhynchus parvulus (bird)
- Camelus dromedarius (Arabian camel)
- Cannabis sativa (hemp)
- Chanos chanos (milkfish)
Continue reading “August-October 2019 RefSeq annotations: mouse, firefly and more”
May-July 2019 RefSeq annotations include newly annotated organisms like octopus, two-lined caecelian
Recently, the NCBI Eukaryotic Genome Annotation Pipeline has released new annotations in RefSeq for the following organisms:
New human genome annotation release with MANE Select and other improvements!
There’s a new RefSeq annotation available for the human genome, and it’s quite an update!
About the release
Annotation release 109.20190607 is the first release of our new bimonthly annotation schedule as announced in a previous post. The annotated sequences are the latest sequences for the GRCh38, patch 13 assembly, GRCh38.p13 (GCF_000001405.39). The chromosome backbone sequences remain the same, but we’ve added 45 patch sequences representing novel and improved sequences that the Genome Reference Consortium will incorporate into the primary assembly in the future. The new annotation places the latest curated RefSeq transcripts and functional elements on the genome but keeps the same model dataset as in annotation release 109 except when the models have been replaced by curated RefSeqs or other review. We are also flagging MANE and other RefSeq Select transcripts. Continue reading for more details on these improvements below. You can download the updated annotation here!
Continue reading “New human genome annotation release with MANE Select and other improvements!”
March-April 2019 RefSeq eukaryotic annotations
In March and April, the NCBI Eukaryotic Genome Annotation Pipeline released new annotations in RefSeq for the following organisms:
Continue reading “March-April 2019 RefSeq eukaryotic annotations”
Human genome annotation will be updated every 2 months
NCBI will be updating the human genome RefSeq annotation more frequently to incorporate improvements made to genes and transcripts by RefSeq curation experts. Faster updates will allow us to include the latest datasets.
In the past, we’ve produced a full re-annotation of the human genome about once a year. The last full annotation, Homo sapiens Annotation Release 109, was in March 2018. A full annotation is produced by two main processes:
Continue reading “Human genome annotation will be updated every 2 months”