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).
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elements on the genome but keeps the same model dataset as in annotation release 109 except when the models have been replaced by curated RefSeqs or other review.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!
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: