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Streamlined analysis of duplex sequencing data with Du Novo.

ABSTRACT: Duplex sequencing was originally developed to detect rare nucleotide polymorphisms normally obscured by the noise of high-throughput sequencing. Here we describe a new, streamlined, reference-free approach for the analysis of duplex sequencing data. We show the approach performs well on simulated data and precisely reproduces previously published results and apply it to a newly produced dataset, enabling us to type low-frequency variants in human mitochondrial DNA. Finally, we provide all necessary tools as stand-alone components as well as integrate them into the Galaxy platform. All analyses performed in this manuscript can be repeated exactly as described at http://usegalaxy.org/duplex .

SUBMITTER: Stoler N

PROVIDER: S-EPMC5000403 | biostudies-literature | 2016 Aug

REPOSITORIES: biostudies-literature

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Streamlined analysis of duplex sequencing data with Du Novo.

Stoler Nicholas N Arbeithuber Barbara B Guiblet Wilfried W Makova Kateryna D KD Nekrutenko Anton A

Genome biology 20160826 1

Duplex sequencing was originally developed to detect rare nucleotide polymorphisms normally obscured by the noise of high-throughput sequencing. Here we describe a new, streamlined, reference-free approach for the analysis of duplex sequencing data. We show the approach performs well on simulated data and precisely reproduces previously published results and apply it to a newly produced dataset, enabling us to type low-frequency variants in human mitochondrial DNA. Finally, we provide all necess ...[more]

PMID: 27566673

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