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Faster SARS-CoV-2 sequence validation and annotation for GenBank using VADR.

Eric P Nawrocki1

  • 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894 USA.

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|May 13, 2022
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Summary

The Viral Annotation DefineR (VADR) software was updated to rapidly annotate SARS-CoV-2 sequences. This enhanced VADR is 1000x faster, efficiently processing millions of viral sequences for GenBank.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Virology

Background:

  • The initial VADR software (v1.0) struggled with the high volume and ambiguous nucleotides of SARS-CoV-2 sequences submitted to GenBank.
  • Processing millions of SARS-CoV-2 sequences required significant time and computational resources, hindering efficient annotation.

Approach:

  • Updated VADR software to handle long stretches of ambiguous 'N' nucleotides by temporarily replacing them.
  • Optimized core processing steps using blastn and glsearch, significantly reducing memory usage and increasing speed.
  • Implemented parallel processing capabilities to manage large-scale SARS-CoV-2 data efficiently.

Key Points:

  • The enhanced VADR software achieves nearly 1000x speed improvement for SARS-CoV-2 sequence annotation.
  • Memory requirements were reduced from 64Gb to 2Gb per thread, enabling efficient processing on standard hardware.
  • Successfully processed over 1.5 million SARS-CoV-2 sequences since June 2020.

Conclusions:

  • The updated VADR (version 1.4.1) is now capable of handling the high throughput of SARS-CoV-2 sequence submissions to GenBank.
  • The software's efficiency and speed make it a valuable tool for ongoing viral surveillance and annotation efforts.
  • VADR is freely available for local installation, supporting broader research and public health initiatives.