title: 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 .
authors: Graduate Program in Bioinformatics and Genomics, The Huck Institutes for the Life Sciences, Penn State University, 505 Wartik Lab, University Park, PA, 16802, USA.
authors: Nicholas
authors: N
authors: Stoler
authors: Institute of Biophysics, Johannes Kepler University, Linz, Austria.
authors: Barbara
authors: B
authors: Arbeithuber
authors: Graduate Program in Bioinformatics and Genomics, The Huck Institutes for the Life Sciences, Penn State University, 505 Wartik Lab, University Park, PA, 16802, USA.
authors: Wilfried
authors: W
authors: Guiblet
authors: Department of Biology, Penn State University, 310 Wartik Lab, University Park, PA, 16802, USA. kdm16@psu.edu.
authors: Kateryna D
authors: KD
authors: Makova
authors: Graduate Program in Bioinformatics and Genomics, The Huck Institutes for the Life Sciences, Penn State University, 505 Wartik Lab, University Park, PA, 16802, USA. aun1@psu.edu.|Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, USA. aun1@psu.edu.
authors: Anton
authors: A
authors: Nekrutenko
mesh_terms: D004272:DNA, Mitochondrial / Q000235:genetics*; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software
chemical_list: D004272:DNA, Mitochondrial
keywords: Duplex sequencing; Genomic data analysis; Low frequency polymorphism discovery; Next generation sequencing