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.

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