CarrierSeq: a sequence analysis workflow for low-input nanopore sequencing
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12859_2018_Article_2124.pdf
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Author(s)
Hachey, Julie
Ruvkun, Gary
Mojarro, Angel
Zuber, Maria
Carr, Christopher E.
Date Issued
March 2018
Journal
BMC Bioinformatics
Publisher
BioMed Central
Citation
Mojarro, Angel et al. "CarrierSeq: a sequence analysis workflow for low-input nanopore sequencing." BMC Bioinformatics 19 (March 2018):108 © 2018 The Authors
Version
Final published version
Abstract
Background
Long-read nanopore sequencing technology is of particular significance for taxonomic identification at or below the species level. For many environmental samples, the total extractable DNA is far below the current input requirements of nanopore sequencing, preventing “sample to sequence” metagenomics from low-biomass or recalcitrant samples. Results
Here we address this problem by employing carrier sequencing, a method to sequence low-input DNA by preparing the target DNA with a genomic carrier to achieve ideal library preparation and sequencing stoichiometry without amplification. We then use CarrierSeq, a sequence analysis workflow to identify the low-input target reads from the genomic carrier. We tested CarrierSeq experimentally by sequencing from a combination of 0.2 ng Bacillus subtilis ATCC 6633 DNA in a background of 1000 ng Enterobacteria phage λ DNA. After filtering of carrier, low quality, and low complexity reads, we detected target reads (B. subtilis), contamination reads, and “high quality noise reads” (HQNRs) not mapping to the carrier, target or known lab contaminants. These reads appear to be artifacts of the nanopore sequencing process as they are associated with specific channels (pores).
Conclusion
By treating sequencing as a Poisson arrival process, we implement a statistical test to reject data from channels dominated by HQNRs while retaining low-input target reads.
MIT Department
Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences
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Creative Commons Attribution
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DOI of Published Version
https://doi.org/10.1186/s12859-018-2124-3
