Tag: Sequence Read Archive (SRA)

Petabyte-Scale Sequence Search: Metagenomics Benchmarking Codeathon Highlights

The National Institutes of Health (NIH) Office of Data Science Strategy (ODSS), the National Library of Medicine’s (NLM’s) National Center for Biotechnology and Information (NCBI), and the Department of Energy’s (DOE’s) Office of Biological and Environmental Research (BER) hosted scientists from around the world for a virtual Petabyte-Scale Sequence Search: Metagenomics Benchmarking Codeathon. The codeathon, held September 27-October 1, 2021, attracted experts from national laboratories including the Los Alamos National laboratory, research institutions including the Joint Genome Institute, and students from universities across the world to develop benchmarking approaches to address challenges in conducting large-scale analyses of metagenomic data.

Continue reading “Petabyte-Scale Sequence Search: Metagenomics Benchmarking Codeathon Highlights” →

NCBI on YouTube: Customize MSA Viewer, SciENcv, plants and RNA-Seq data, Datasets and PubMed

Missed a few videos on YouTube? Here’s the latest from our channel.

Customize the MSA Viewer to Make Your Analysis Easier

We’re constantly improving the Multiple Sequence Alignment (MSA) Viewer. This video demonstrates several new and popular features, including the ability to change data columns, hide selected rows, analyze polymorphisms, and more.

Continue reading “NCBI on YouTube: Customize MSA Viewer, SciENcv, plants and RNA-Seq data, Datasets and PubMed” →

View GEO, SRA, or dbGaP data tracks in NCBI’s Genome Data Viewer

Did you know that you can see epigenomic or other experimental data in NCBI’s Genome Data Viewer (GDV)?

You can easily add aligned study results from GEO, SRA, and dbGaP as data tracks to GDV browser view. Just go to the Tracks button on the toolbar and select the menu option to Configure Tracks. Navigate to the ‘Find Tracks’ tab on the pop-up Configure panel (Figure 1).

screenshot of genome data browser, showing 'Tracks' menu and 'Find Tracks' tab — **Figure 1.** Go to the ‘Tracks’ menu on the browser toolbar and select ‘Configure Tracks’ option. This will launch a panel where you can add, configure, remove, and search for data tracks. Go to the ‘Find Tracks’ tab to search for tracks to add to your browser view. Note: spaces act as AND operators in the search, and wildcards are accepted.

Continue reading “View GEO, SRA, or dbGaP data tracks in NCBI’s Genome Data Viewer” →

The Sequence Read Archive slims down your data with SRA Lite

In response to your requests for compact and faster-to-deliver data, NIH’s Sequence Read Archive (SRA) now offers a new data format – SRA Lite (Figure 1). SRA Lite supports reliable and faster data transfer, downloads, and analysis using current tools. SRA Lite replaces the submitted base quality score (BQS) with a simplified read quality score, reducing the average read size by ~60% for more efficient analysis and storage of large datasets. This format was designed to reflect improvements in next-generation sequencing that include increases in average read length and sequence coverage. Indeed, the data has improved enough that that removing some quality scores increase genotype accuracy (PMCID: PMC4439189).

Figure 1. FASTQ dumped from SRA Lite format and the SRA configuration dialog. The FASTQ has the quality score for each base set to 30 (‘?’ in the ASCII encoding). Select “Prefer SRA Lite files with simplified base Quality scores” in the SRA configuration dialog to use SRA Lite. Continue reading “The Sequence Read Archive slims down your data with SRA Lite” →

Tackling Petabyte Scale Sequence Search Challenges

The volume of biological data being generated by the scientific community is growing exponentially, reflecting technological advances and research activities. This increase in available data has great promise for pushing scientific discovery but also introduces new challenges that scientific communities need to address. The National Institutes of Health’s (NIH) Sequence Read Archive (SRA), which is maintained by the National Library of Medicine’s National Center for Biotechnology Information (NCBI), is a rapidly growing public database that researchers use to improve scientific discovery across all domains of life. As part of the Science and Technology Research Infrastructure for Discovery, Experimentation, and Sustainability (STRIDES) Initiative, over 36 petabytes of “next generation” (raw and SRA-formatted) sequencing data is accessible to anybody via two cloud service providers.

To help address the challenges of conducting large-scale analysis of -omic data in the SRA and similar databases, the Department of Energy (DOE) Office of Biological and Environmental Research (BER), the NIH Office of Data Science Strategy (ODSS), and NCBI, held a virtual workshop on June 8, 2021, on Emerging Solutions in Petabyte Scale Sequence Search. The workshop brought together experts from DOE national labs, research institutions, and universities across the world.

SRA data growth over time. Databases like the NIH Sequence Read Archive are growing rapidly and are used extensively by scientific communities. As these databases grow, so do their potential scientific value, but work must be done to ensure ease of access.

Continue reading “Tackling Petabyte Scale Sequence Search Challenges” →

Aug 18 Webinar: Finding Data for your Research Organism: Plants and RNA-Seq data

Join us on August 18, 2021 at 12PM eastern time for the second webinar on finding data for your non-model research organism. In this webinar, you will learn how to use NCBI’s web resources to get data for a plant species, the black cottonwood. You will see how to find, access, and analyze gene and sequence data from Datasets and other NCBI web resources, as well as sample metadata and gene expression RNA-Seq data from SRA and the SRA Run Selector. You will also see an example that highlights how to use and analyze these data in a typical workflow set up in a Jupyter notebook that uses the NCBI next-gen aligner Magic-BLAST to get relative gene expression levels across samples.

Date and time: Wed, August 18, 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.

NCBI events at the Bioinformatics Open Science Conference 2021 (BOSC 2021)

Come visit us virtually to learn about new NCBI data access, tools and best practices at the Bioinformatics Open Science Conference part of the ISMB/ECCB online conference from July 29 – 30, 2021. We will be presenting virtual posters on NCBI resources, offering a Birds of a Feather discussion, and participating in the BOSC (CoFest) following the conference where you can take part in a hands-on evaluation of ElasticBLAST.

NCBI Posters, July 29, 2021, 11:20 – 12:20 PM EDT

All posters will be presented on Thursday afternoon. You can see complete abstracts on the ISMB/ECCB BOSC schedule.

Nuala O’Leary will talk about NCBI Datasets, a new resource for fast, easy access to NCBI sequence data. You will learn about the new interface and new tools to access reference genomes, genes, and orthologs using web-based and programmatic tools.

Adelaide Rhodes will present Open access NCBI cloud resources to accelerate scientific insights where you can learn about recent developments in transferring > 20 petabytes of NCBI Sequence Read Archive (SRA) data to the cloud.

Deacon Sweeney will describe the web RAPT service for assembling and annotating bacterial genomes at the click of a button in RAPT, The Read assembly and Annotation Pipeline Tool: building a prokaryotic genome annotation package for users of all backgrounds.

Roberto Vera Alvarez will talk about best practices for using cloud tools for transcriptomics in his poster Transcriptome annotation in the cloud: complexity, best practices, and cost.

Greg Boratyn will discuss improvements to the BLAST-based short read aligner, Magic-Blast, in Recent improvements in Magic-BLAST 1.6.

Visit Christiam Camacho’s poster ElasticBLAST: Using the power of the cloud to speed up science to get an introduction to ElasticBLAST, a Kubernetes-based approach for high throughput BLAST tasks. Join us following the conference in the CoFest to try out ElasticBLAST yourself and provide input. See the section on the CoFest below and our companion post.

Birds of a Feather, July 29, 2021, 11:20 – 12:20 PM EDT

We will host a Birds of Feather public feedback session on Thursday, where you can provide feedback and participate in discussions on all aspects of NCBI’s new data access options: NCBI Datasets, SRA, BLAST, and the Genome Data Viewer (GDV) — our genome browser for sequence visualization. We welcome your input! Come and see us!

CollaborationFest (CoFest), July 31 – August 1, 2021

The ElasticBlast team will attend the BOSC CoFest following the conference. Sign up to participate on July 31 and August 1 to get an in-depth orientation and opportunity to test the capabilities of ElasticBlast on the Amazon Web Services (AWS) cloud. You do not have to register for the conference to attend the CoFest. See our post on the CoFest for more information.