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Title: Real-Time Selective Sequencing with RUBRIC: Read Until with Basecall and Reference-Informed Criteria

Journal Article · · Scientific Reports
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Abstract The Oxford MinION, the first commercial nanopore sequencer, is also the first to implement molecule-by-molecule real-time selective sequencing or “Read Until”. As DNA transits a MinION nanopore, real-time pore current data can be accessed and analyzed to provide active feedback to that pore. Fragments of interest are sequenced by default, while DNA deemed non-informative is rejected by reversing the pore bias to eject the strand, providing a novel means of background depletion and/or target enrichment. In contrast to the previously published pattern-matching Read Until approach, our RUBRIC method is the first example of real-time selective sequencing where on-line basecalling enables alignment against conventional nucleic acid references to provide the basis for sequence/reject decisions. We evaluate RUBRIC performance across a range of optimizable parameters, apply it to mixed human/bacteria and CRISPR/Cas9-cut samples, and present a generalized model for estimating real-time selection performance as a function of sample composition and computing configuration.

Research Organization:
Sandia National Lab. (SNL-CA), Livermore, CA (United States); Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
Sponsoring Organization:
USDOE National Nuclear Security Administration (NNSA)
Grant/Contract Number:
AC04-94AL85000
OSTI ID:
1645170
Alternate ID(s):
OSTI ID: 1487413; OSTI ID: 1559518
Report Number(s):
SAND-2018-10906J; SAND2019-9606J; 11475; PII: 47857
Journal Information:
Scientific Reports, Journal Name: Scientific Reports Vol. 9 Journal Issue: 1; ISSN 2045-2322
Publisher:
Nature Publishing GroupCopyright Statement
Country of Publication:
United Kingdom
Language:
English
Citation Metrics:
Cited by: 12 works
Citation information provided by
Web of Science

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Figures / Tables (24)

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