June 2 Webinar: Quickly upload and view your own data in genomic context at NCBI

June 2 Webinar: Quickly upload and view your own data in genomic context at NCBI

Join us on June 2, 2021 at 12PM eastern time to learn how to how to upload and display your own genomic data in the context of annotated genome assemblies. You will use the Genome Data Viewer and the Sequence viewer to visualize your own uploaded data (indexed BAM, VCF, BED, wig, GFF formats), data from public track hubs, and your BLAST and Primer-BLAST results. You will also learn to take advantage of features of the viewers including optimizing display settings, sharing a view with collaborators, exporting images, and downloading genes or other features in the view.

  • Date and time: Wed, June 2, 2021 12:00 PM – 12:45 PM EDT
  • Register

After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI webinars playlist on the NLM YouTube channel. You can learn about future webinars on the Webinars and Courses page.

Magic-BLAST version 1.6.0 is here!

Magic-BLAST version 1.6.0 is here!

We’ve just released  a new version (1.6.0) of Magic-BLAST, the BLAST-based next-gen alignment tool, with these improvements:

  • Usage reporting — you can help improve Magic-BLAST by sharing limited information about your search. The BLAST User Manual has details on the information collected, how it is used, and how to opt-out.
  • Magic BLAST can access NCBI SRA next-gen reads from the cloud when  you use the -sra or -sra_batch options.  See the Magic-BLAST cookbook for more details.
  • NCBI taxonomy IDs are reported in SAM output if they are present in the target BLAST database.
  • You can get unaligned reads reported separately from the aligned ones by using the -out_unaligned <file name> option.  You can also select the format ( SAM, tabular, or FASTA) with the -unaligned_fmt option. The default format is the same as one for the main report .

The version 1.6.0 executables are available from the NCBI FTP site.  See the release notes , the NCBI GitHub site , and the Magic-BLAST publication for more information.

Vertebrate Genome Project genome assemblies annotated by NCBI

Vertebrate Genome Project genome assemblies annotated by NCBI

NCBI is an active partner of the Vertebrate Genomes Project (VGP), who recently published a series of papers on the initial results of their efforts to sequence all 70,000 vertebrate species.  See the VGP press release  for more details. To date, this project has submitted over 130 diploid chromosome-level assemblies to NCBI’s GenBank  and the European Nucleotide Archive.  NCBI has annotated 94 of the VGP assemblies from 85 species using the NCBI Eukaryotic Genome Annotation Pipeline.

These sequence and annotation data are available through NCBI web resources including Gene, Assembly, Nucleotide, Protein, and Datasets and are included in the GenBank and RefSeq releases. You can browse the assemblies in the Genome Data Viewer  and  download metadata, sequence, and annotation data for the latest assemblies in the VGP BioProject using the NCBI Datasets command-line tools  as shown below. Continue reading “Vertebrate Genome Project genome assemblies annotated by NCBI”

Prokaryotic representative genomes update–over 900 new species!

We are happy to announce an updated bacterial and archaeal representative genome collection! We have selected 13,835 among 214,000 prokaryotic RefSeq assemblies to represent their respective species. The collection has increased by 6% since December 2020. About 950 species are represented for the first time, 476 species are represented by a better assembly, and 170 species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment.

Continue reading “Prokaryotic representative genomes update–over 900 new species!”

Assemble and annotate your prokaryotic genomes with RAPT

Do you need an easy way to analyze a bacterium you just isolated? The latest version of NCBI’s Read assembly and Annotation Pipeline Tool (RAPT) is a pilot web service for the assembly and gene annotation of public or private Illumina genomic reads sequenced from bacterial or archaeal isolates.

We’ll be giving a webinar on webRAPT on May 19 where you can learn more, but you can test it out now.

Get started with the click of a button

RAPT is simple to use.

1. If you’re working with NIH’s Sequence Read Archive (SRA) and have an SRA accession, enter it in the first box below (Figure 1a) or upload a file of sequencing reads in the second box (Figure 1b).

screenshot of webRAPT submission; enter SRA accession number on the left or upload files on the right
Figure 1. 1a, on the left. Enter an SRA run accession (starting with SRR, DRR or ERR) in the text box on the left if you wish to assemble reads that are already public and press submit. If you are providing a read set that is not in SRA, use the box on the right, shown in 1b. Enter the organism name (genus only or genus species known to NCBI Taxonomy) in the “Organism” field. Click “One file” if all reads for the run are in a single file. This file can contain single-end reads or paired-end reads with reads of a pair adjacent to each other in the file (interleaved). Upload the sequencing reads using the “Choose file” button. Click “Two files” to provide forward and reverse reads from a paired-end library in two separate files. Upload the forward and reverse files using the “Choose Forward Reads File” and “Choose Reverse Reads File” buttons. Then press submit.

 

 

Continue reading “Assemble and annotate your prokaryotic genomes with RAPT”

May 19 Webinar: Using the new web RAPT service to assemble and annotate prokaryotic genomes

May 19 Webinar: Using the new web RAPT service to assemble and annotate prokaryotic genomes

Join us on May 19, 2021 at 12PM eastern time to learn how to use the new  RAPT pilot service to assemble and annotate public or private Illumina genomic reads sequenced from bacterial or archaeal isolates at the click of a button. RAPT consists of two major components, the genome assembler SKESA and the Prokaryotic Genome Annotation Pipeline (PGAP), and produces an annotated genome of quality comparable to RefSeq in a couple of hours.

  • Date and time: Wed, May 19, 2021 12:00 PM – 12:45 PM EDT
  • Register

After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI webinars playlist on the NLM YouTube channel. You can learn about future webinars on the Webinars and Courses page.

A dedicated SARS-CoV-2 BioSample submission package in the NCBI Submission Portal

During the COVID-19 pandemic, it is critical to collect descriptive information about the provenance and attributes of SARS-CoV-2 genomic samples so that the course of the virus may be tracked and analyzed. The NCBI Submission Portal now includes a dedicated BioSample submission package to help further improve the quality and richness of submitted SARS-CoV-2 sample metadata. The SARS-CoV-2 clinical or host-associated package presents a framework and standardized fields for submitters to provide attributes considered useful for the rapid analysis and surveillance of SARS-CoV-2 clinical and host-associated cases. For example, mandatory attributes include collection date and geographic location, while suggested but optional attributes include date of SARS-CoV-2 vaccination, vaccine received, and host disease outcome.

a mock-up of a SARS submission shows fields for important metadata
Figure 1. This mock-up shows mandatory attributes like collection date and geographic location, as well as suggested attributes like date of vaccination and host disease outcome.

Continue reading “A dedicated SARS-CoV-2 BioSample submission package in the NCBI Submission Portal”

NCBI at CSHL Biology of Genomes, May 11 – 14, 2021

NCBI at CSHL Biology of Genomes, May 11 – 14, 2021

NCBI staff will be presenting virtual posters at the Cold Spring Harbor Laboratory  Biology of Genomes Meeting, May 11 -14, 2021. The posters will cover the following topics: 1) a cloud-ready suite of tools (PGAP, RAPT , and SKESA) for assembling and annotating prokaryotic genomes,  2) Datasets — a new set of services for downloading genome assemblies and annotations, and 3) updates on NCBI RefSeq eukaryotic genome annotation, and the Genome Data Viewer (GDV). Read more below for the full abstracts.

The virtual poster gallery opens Tuesday, May 11 at 9:00 a.m. with dedicated time for poster viewing and discussion at 1:00 to 2:00 p.m. through Slack each day. The poster gallery will be open for entire the conference and remain available for six weeks afterwards.  Continue reading “NCBI at CSHL Biology of Genomes, May 11 – 14, 2021”

NCBI on YouTube: Tips for My Bibliography, Genome Data Viewer and more

Missed our latest YouTube videos? Scroll down to see what we’ve been up to.

Add Preprint Citations in My Bibliography

The National Institutes of Health encourages investigators to post preprints to public repositories in order to speed the dissemination and enhance the rigor of their work. This video demonstrates how to add preprint citations to My Bibliography.

Continue reading “NCBI on YouTube: Tips for My Bibliography, Genome Data Viewer and more”