Tag: SRA Toolkit

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” →

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.

SRA cloud sequences hold the promise of additional discoveries related to COVID-19

We recently announced that we made all of the Sequence Read Archive (SRA) publicly available on two cloud platforms. This archive of genetic sequences is a treasure trove of information and the cloud environments provide high-performance computing capabilities via a GCP or AWS account – right from your own device. High-throughput sequencing has made generating data extremely fast and inexpensive, which has fueled the rapid growth of SRA. Putting it on the cloud makes it possible to analyze “the high-throughput, unassembled sequence data, across all such sequences”.

So, what are some of the potential discoveries that await? To investigate some of the possibilities, we have held a series of codeathons to see if known and unknown viruses could be found lurking within SRA cloud datasets. Spoiler alert – they are! And just recently, a team from Stanford reported that they were able to identify a 2019-nCoV-like Coronavirus in pangolins by examining data sets identified via a meta-metagenomic search of SRA and downloaded using the SRA Toolkit. One challenge this team faced was downloading the datasets: 2.5TB corresponding to approximately 10¹³ bases took over 48 hours to gather. How might cloud-based SRA tools have made this task easier/faster? Here’s how:

BigQuery: allows native cloud programmatic access to and search based on SRA metadata in the cloud. SRA Toolkit enables retrieval and reading of sequencing files from the SRA datasets in the cloud and writing files into the same format, respectively.
Coming soon to the cloud are tools for large scale BLAST processing for a Read Alignment and Annotation Pipeline Tool (RAPT). These tools allow the data to be analyzed directly in the cloud, eliminating the need for download to local storage for analysis.
Also in the works is a mechanism to provide better access to taxonomic content of SRA runs as calculated by NCBI tools.

We are continually adding new functionality to better support your cloud workflows and are happy to help! Contact us at sra@ncbi.nlm.nih.gov if you have questions or need help getting started. If you need assistance setting up GCP or AWS, please follow the steps in our how-to videos on YouTube.

Users of the SRA FTP site: Try the SRA Toolkit!

If you download data from the SRA (Sequence Read Archive) FTP site, we would encourage you to try the SRA Toolkit. This is particularly true if you use the SRA Fuse/FTP site at ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant, which the SRA team will decommission on December 1, 2019.

The SRA Toolkit offers several advantages for downloading SRA data, including greater flexibility in specifying the data you need as well as access to public SRA data in the cloud. If you’re new to the Toolkit, you may want to start with these instructions.

If you have any questions or concerns about downloading SRA data, please contact sra@ncbi.nlm.nih.gov. We’d love to hear from you!

SRA Toolkit: the SRA database at your fingertips

The Sequence Read Archive (SRA), NCBI’s largest growing repository of molecular data, archives raw sequencing data and alignment information from high-throughput sequencing platforms, including Roche 454 GS Systems®, Illumina’s Genome Analyzer®, and Complete Genomics® systems.

Researchers commonly use SRA data to make discoveries via comparison of data sets. Data sets can be compared through the SRA web interface, but if you want to integrate these downloads and file conversions into an already existing pipeline, or you simply prefer using a command-line interface, we recommend using the SRA Toolkit.

Continue reading “SRA Toolkit: the SRA database at your fingertips” →