A de novo DNA Sequencing and Variant Calling Algorithm for Nanopores

BioRxiv : the Preprint Server for Biology
Tamas Szalay, Jene A Golovchenko

Abstract

The single-molecule accuracy of nanopore sequencing has been an area of rapid academic and commercial advancement, but remains insufficient for the de novo analysis of genomes. We introduce here a novel algorithm for the error correction of nanopore data, utilizing statistical models of the physical system in order to obtain high accuracy de novo sequences at a range of coverage depths. We demonstrate the technique by sequencing M13 bacteriophage DNA to 99% accuracy at moderate coverage as well as its use in an assembly pipeline by sequencing λ DNA at a range of coverages. We also show the algorithm’s ability to accurately classify sequence variants at far lower coverage than existing methods.

Related Concepts

Bacteriophage M13
Genome
Nucleic Acid Sequencing
Human DNA Sequencing
Sequencing
Bacillus sp. M13
Sequence Determinations, DNA
Analysis
DNA
Small Molecule

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