Reliable and accurate diagnostics from highly multiplexed sequencing assays

Sci Rep. 2020 Dec 10;10(1):21759. doi: 10.1038/s41598-020-78942-7.


Scalable, inexpensive, and secure testing for SARS-CoV-2 infection is crucial for control of the novel coronavirus pandemic. Recently developed highly multiplexed sequencing assays (HMSAs) that rely on high-throughput sequencing can, in principle, meet these demands, and present promising alternatives to currently used RT-qPCR-based tests. However, reliable analysis, interpretation, and clinical use of HMSAs requires overcoming several computational, statistical and engineering challenges. Using recently acquired experimental data, we present and validate a computational workflow based on kallisto and bustools, that utilizes robust statistical methods and fast, memory efficient algorithms, to quickly, accurately and reliably process high-throughput sequencing data. We show that our workflow is effective at processing data from all recently proposed SARS-CoV-2 sequencing based diagnostic tests, and is generally applicable to any diagnostic HMSA.

MeSH terms

  • COVID-19 Nucleic Acid Testing*
  • COVID-19* / diagnosis
  • COVID-19* / genetics
  • Humans
  • Molecular Diagnostic Techniques*
  • Real-Time Polymerase Chain Reaction*
  • SARS-CoV-2 / genetics*