Tag: RefSeq

New annotations in RefSeq

New annotations in RefSeq

In June and July, the NCBI Eukaryotic Genome Annotation Pipeline released twenty-six new annotations in RefSeq for the following organisms:

  • Anopheles coluzzii (mosquito)
  • Anopheles funestus (African malaria mosquito)
  • Astyanax mexicanus (Mexican tetra)
  • Athalia rosae (coleseed sawfly)
  • Bactrocera dorsalis (oriental fruit fly)
  • Brassica napus (rape)
  • Brienomyrus brachyistius (bony fish)
  • Canis lupus dingo (dingo) (pictured)
  • Caretta caretta (Loggerhead turtle)
  • Dendroctonus ponderosae (mountain pine beetle)
  • Epinephelus fuscoguttatus (brown-marbled grouper)
  • Lagopus muta (rock ptarmigan)
  • Marmota marmota marmota (Alpine marmot)
  • Nematostella vectensis (starlet sea anemone)
  • Ostrea edulis (bivalve)
  • Panthera uncia (snow leopard)
  • Plutella xylostella (diamondback moth)
  • Pyrus x bretschneideri (Chinese white pear)
  • Rhincodon typus (whale shark)
  • Rhipicephalus sanguineus (brown dog tick)
  • Solanum stenotomum (eudicot)
  • Solanum verrucosum (eudicot)
  • Sphaerodactylus townsendi (lizard)
  • Stegostoma fasciatum (shark)
  • Triticum urartu (monocot)
  • Ziziphus jujuba (common jujube)

Continue reading “New annotations in RefSeq”

Foreign Contamination Screen (FCS) tool for GenBank submissions

Foreign Contamination Screen (FCS) tool for GenBank submissions

We are excited to introduce a Foreign Contamination Screen (FCS) tool that you can now run yourself, with enhanced contaminant detection sensitivity to improve your genome assemblies and facilitate high-quality data submissions to GenBank. If you submit genome assembly data to GenBank, the FCS tool is for you!

What is the FCS tool?

FCS, a quality assurance process used to make data suitable for submission, consists of two parts: FCS-adaptor and FCS-GX. FCS-adaptor searches for short sequences that are used as part of the lab preparation process and sometimes wind up in the final assembly by mistake. FCS-GX searches for sequences from a wide range of organisms including bacteria, fungi, protists, viruses, and others to identify sequences that don’t look like they are from the intended organism. In each case, you receive a report of the coordinates and identities of potential contaminants to be reviewed and removed (see Figure 1 for a sample report of the FCS-GX summary output). Both tools are designed to screen both eukaryote and prokaryote genomes.

Figure 1. FCS-GX report showing the summary of contamination identified in a tomato genome. The output indicates there are 83 sequences, adding up to 381 kb total length, to be removed from a mix of insect, fungal, and bacterial sources.

How do I use FCS?

FCS is available from GitHub. Simply download the two programs (FCS-adaptor and FCS-GX), and follow a few steps as outlined in the Quickstart. Both tools are also easy and inexpensive to run on commercial clouds such as Amazon Web Services (AWS) or Google Cloud Platform (GCP), and can screen genomes in a fraction of the time of other approaches. 

Why is FCS important?

Having high quality data available for analysis is necessary in order to arrive at accurate conclusions during research. With FCS, rapid detection of contaminants from foreign organisms in assembled genomes ensures that high value data is being provided for submission and available for reuse. We’ve already used FCS-GX to remove over one hundred megabases of contaminants and thousands of erroneous genes and proteins from previously submitted eukaryote genomes to make the data more useful for all. 

We want to hear from you!

We will update the FCS tool based on your feedback, so try it out and let us know what you think. Please contact us with comments and suggestions.

FCS is part of the NIH Comparative Genomics Resource (CGR), an NLM project to establish an ecosystem to facilitate reliable comparative genomics analyses for all eukaryotic organisms.

Join our mailing list to keep up to date with FCS and other CGR news.

RefSeq Release 213

RefSeq Release 213

RefSeq Release 213 is now available online, from the FTP site and through NCBI’s Entrez programming utilities, E-utilities.

This full release incorporates genomic, transcript, and protein data available as of July 11, 2022, and contains 321,282,996 records, including 234,520,053 proteins, 45,781,716 RNAs, and sequences from 121,461 organisms. The release is provided in several directories as a complete dataset and also as divided by logical groupings. Continue reading “RefSeq Release 213”

NLM’s all-new NCBI Datasets genome table is now available

NLM’s all-new NCBI Datasets genome table is now available

We are excited to introduce new and useful updates to the Datasets genome table that let you quickly find and download a genome dataset including genome, transcript and protein sequence, annotation, and a data report.

The new genome table includes many new features and benefits (see Figure 1). With the new genome table you can:

  • Find all current genomes, including metagenomes
  • View multiple taxa such as birds and bees, or polyphyletic groups like fish
  • Easily find genomes with NCBI RefSeq annotations
  • Get more accurate genome counts, since each row now represents a single genome with GenBank and RefSeq accessions for that genome in the same row
  • Customize your downloads to include either GenBank or RefSeq files, or both
  • Download tables or data packages

Continue reading “NLM’s all-new NCBI Datasets genome table is now available”

New RefSeq annotations are available!

New RefSeq annotations are available!

In April and May, the NCBI Eukaryotic Genome Annotation Pipeline released twenty-eight new annotations in RefSeq for the following organisms:

Announcing an updated prokaryotic representative genomes collection with 706 new species!

Announcing an updated prokaryotic representative genomes collection with 706 new species!

An updated bacterial and archaeal representative genomes collection is available! A total of 16,105 assemblies among the 249,000 prokaryotic assemblies in RefSeq were selected to represent their respective species. The collection has grown by 3.7% since January 2022. A total of 706 species are represented for the first time. In addition, 186 species are represented by a better assembly, and 124 species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment.

We updated the database on the Microbial Nucleotide BLAST page as well as the basic nucleotide BLAST RefSeq Representative genomes database (fourth in the menu) to reflect these changes. Finally, remember that you can now run BLAST searches against the proteins annotated on representative genomes (second in the menu). See more info here.

New in RAPT: Better taxonomic assignment and GO annotation

New in RAPT: Better taxonomic assignment and GO annotation

We are excited to announce two improvements to the Read assembly and Annotation Pipeline Tool (RAPT), which allows you to assemble genomic reads for bacterial or archaeal isolates and annotate their genes at the click of a button.

Improved taxonomic assignment

Now RAPT verifies the scientific name you provide with the reads, and corrects it as needed with the Average Nucleotide Identity (ANI) tool, which compares your genome to type strain assemblies in GenBank to place it in the taxonomic tree. So, even if you only have a rough idea of the species you have sequenced, input datasets tailored to your genome will be used for the annotation and you will get the best possible gene set from RAPT. Continue reading “New in RAPT: Better taxonomic assignment and GO annotation”

Announcing Human Annotation Release 110

Announcing Human Annotation Release 110

The annotation of human assemblies GRCh38.p14 and T2T-CHM13v2.0

We are happy to announce the first de novo annotation of human T2T-CHM13v2.0, the gap-less assembly generated by the T2T Consortium, and the full re-annotation of the human reference assembly, GRCh38.p14. We hope the results will serve both the needs of those eager to explore newly sequenced regions of the genome, including telomeres and centromeres, and those interested in refreshing their interpretation of the human reference, in light of recently curated transcripts and new transcriptomic and other data incorporated in the annotation. Continue reading “Announcing Human Annotation Release 110”

Gapless Telomere to Telomere human genome (T2T-CHM13) now available

Gapless Telomere to Telomere human genome (T2T-CHM13) now available

On April 1, 2022, Science published the first complete sequence of a human genome, known as T2T-CHM13. This notable scientific achievement comes two decades after the first human genome release from the Human Genome Project and offers an in situ look at biologically important regions, such as centromeres, telomeres, and segmental duplications, that were previously unassembled. Read on to learn more about how you can access this assembly and related resources at NCBI, or to access any one of the more than 1000 human genome assemblies now in GenBank. Continue reading “Gapless Telomere to Telomere human genome (T2T-CHM13) now available”

RefSeq Release 212 is available!

RefSeq Release 212 is available!

RefSeq Release 212 is now available online, from the FTP site and through NCBI’s Entrez
programming utilities, E-utilities.

This full release incorporates genomic, transcript, and protein data available as of May 2, 2022, and contains 314,915,153 records, including 229,417,182 proteins, 44,805,833 RNAs, and sequences from 119,373 organisms. The release is provided in several directories as a complete dataset and also as divided by logical groupings.

Human genome Annotation Release 110

Annotation Release 110 is the first new annotation of human in four years, including all latest curated RefSeqs, and recalculation of models using over 80M long reads and 9B Illumina RNA-seq reads. AR 110 includes annotation of two human assemblies: Continue reading “RefSeq Release 212 is available!”