Tag: genomics

Improved access to SARS-CoV-2 data

NCBI Datasets has a simple, new way to get Coronoviridae data, including from SARS-CoV-2 (Figure 1). The data package includes genomic, protein and CDS sequences, annotation and a comprehensive data report for all complete genomes. You can also target your search to major taxonomic ranks within Coronaviridae.

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Figure 1 – SARS-CoV-2 page within NCBI Datasets showing statistics as of June 16, 2020.

Interested in a specific protein? The SARS-CoV-2 protein page allows you to choose a protein and download the corresponding sequences, annotation and representative structures from all annotated genomes (Figure 2).

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Figure 2 – SARS-CoV-2 protein page within NCBI Datasets showing annotations on the SARS-CoV-2 reference genome.

Looking for programmatic access? NCBI Datasets offers the same Coronoviridae genomic data and SARS-CoV-2 protein data through a command-line tool and a RESTful API. These tools support additional filtering including the ability to download only those genomes released after a date you specify.

We appreciate your feedback. Try NCBI Datasets and let us know what you think!

May 20 webinar: Exploring SRA metadata in the cloud with BigQuery

May 20 webinar: Exploring SRA metadata in the cloud with BigQuery

Join us on May 20th to learn how to use Google’s BigQuery to quickly search the data from the Sequence Read Archive (SRA) in the cloud to speed up your bioinformatic research and discovery projects. BigQuery is a tool for exploring cloud-based data tables with SQL-like queries. In this webinar, we’ll introduce you to using BigQuery to mine SRA submitter-supplied metadata and the results of taxonomic analysis for SRA runs. You’ll see real-world case studies that demonstrate how to find key information about SRA runs and identify data sets for your own analysis pipelines.

  • Date and time: Wed, May 20, 2020 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 YouTube channel. You can learn about future webinars on the Webinars and Courses page.

Flies Are A-buzzing in RefSeq!

Are you interested in comparative genomics or other studies using Drosophila genomics?

Then don’t miss our online poster #568A at TAGC 2020 Online (no meeting registration required). Also, tune in to the online Q&A session on Monday, April 27 at 12:00 – 12:30 pm EDT.

What’s happening? In coordination with FlyBase, we are transitioning almost all of the RefSeq Drosophila assemblies to annotation produced primarily by NCBI’s eukaryotic genome annotation pipeline. We’ll continue to use the FlyBase annotation for Drosophila melanogaster (soon to be updated to Release 6.32), but we’ll annotate the other species using available RNA-seq datasets and our latest software. This will allow us to provide consistent, high-quality annotations across the full spectrum of Drosophila species, and also rapidly provide annotations as new high-quality assemblies become available. Another benefit is that these annotations will be available in the full suite of NCBI resources, including nucleotide, protein, BLAST, GeneGenome Data Viewer, Genomes, Assembly, and more. You can download these annotation data from the NCBI genomes FTP site or you can try the new NCBI Datasets tool. By special request, we’re making orthology data relative to D. melanogaster available on the Gene FTP site, and plan to expose that data in our public pages in the future.

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April 8 Webinar: Accelerate genomics discovery with SRA in the cloud

April 8 Webinar: Accelerate genomics discovery with SRA in the cloud

On Wednesday, April 8, 2019 at 12 PM, NCBI staff will show you how to leverage the cloud to speed up your research and discovery. You’ll be introduced to new and existing tools and data including BigQuery, SRA Toolkit, and more. You’ll hear about real workflows in the cloud featuring an example of the work NCBI was able to accomplish in the cloud using SRA data and a case study from an SRA cloud customer

By the end of this webinar, you will know where to look for new cloud products from NCBI, access help information to get you started, and will see how to run your analyses efficiently in the cloud.

  • Date and time: Wed, Apr 8, 2020 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 YouTube channel. You can learn about future webinars on the Webinars and Courses page.

View BAM alignments in the NCBI genome browsers and sequence viewers sorted by haplotype tag

NCBI’s genome browsers and graphical sequence viewers now allow you to view BAM alignments sorted by haplotype tag. This option is useful for analyzing variants within a sequenced sample and can help you detect or validate structural variants.GDV_bamsFigure 1. Remote BAM alignment data sorted by haplotype tag in the Genome Data Viewer. The remote BAM file was added through the “User Data and Track Hubs” feature in GDV.  You can load the remote BAM for this example through https://go.usa.gov/xpM9c. The sorted display shows that haplotype 1 contains a significant deletion in this region relative to haplotype 2 and the reference genome assembly. Aligned reads not assigned a haplotype tag in the BAM file are grouped under the heading “haplotype not set” (not shown). 

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December 11 Webinar: Running the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) on your own data

December 11 Webinar: Running the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) on your own data

On Wednesday, December 11, 2019 at 12 PM, NCBI staff will present a webinar that will show you how to use NCBI’s PGAP (https://github.com/ncbi/pgap) on your own data to predict genes on bacterial and archaeal genomes using the same inputs and applications used inside NCBI. You can run PGAP your own machine, a compute farm, or in the Cloud. Plus, you can now submit genome sequences annotated by your copy of PGAP to GenBank.  Attend the webinar to learn more!

  • Date and time: Wed, Dec 11, 2019 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 YouTube channel. You can learn about future webinars on the Webinars and Courses page.

NIH Biomedical Data Science Codeathon in Pittsburgh, Jan 8-10

NIH Biomedical Data Science Codeathon in Pittsburgh, Jan 8-10

NCBI is pleased to announce a Biomedical Data Science Codeathon in collaboration with Carnegie Mellon in Pittsburgh, PA on January 8-10, 2020.

We’re specifically seeking people with experience working with complex diseases, precision medicine, and genomic analyses.  If this describes you, please apply! This event is for researchers, including students and postdocs, who are already engaged in the use of bioinformatics data or in the development of pipelines for large scale genomic analyses from high-throughput experiments. The event is open to anyone selected for the codeathon and willing to travel to Pittsburgh.

Potential topics include:

  • Virus Genome Graph tools
  • Image analysis pipelines
  • RNAseq pipelines
  • Cancer graph genomes
  • Complex Disease Analysis

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Structural Variant Hackathon

NCBI is pleased to announce a Structural Variant Hackathon at the Baylor College of Medicine, Houston Texas, immediately before ASHG on October 11-13, 2019.

We’re specifically looking for folks who have experience in working with structural variants, complex disease, precision medicine, and similar genomic analysis.  If this describes you, please apply! This event is for researchers, including students and postdocs, who are already engaged in the use of bioinformatics data or in the development of pipelines for large scale genomic analyses from high-throughput experiments (please note that the event itself will focus on open access public human data).

Potential topics include:

  • Mapping structural variants to public databases
  • Calculating the heritability of different types of structural variants
  • CNV effect on isoform expression
  • Assembly accuracy for metagenomics
  • Quality assessment in large cohorts

The hackathon runs from 9 am – 6 pm each day, with the potential to extend into the evening hours each day. There will also be optional social events at the end of each day. Working groups of five to six individuals, with various backgrounds and expertise, will be formed into five to eight teams with an experienced leader. These teams will build pipelines and tools to analyze large datasets within a cloud infrastructure. Each day, we will come together to discuss progress on each of the topics, bioinformatics best practices, coding styles, etc.

There will be no registration fee associated with attending this event.

Note: Participants will need to bring their own laptop to this program. No financial support for travel, lodging, or meals is available for this event.

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