title: A Benchmark Study on Error Assessment and Quality Control of CCS Reads Derived from the PacBio RS.
abstract: PacBio RS, a newly emerging third-generation DNA sequencing platform, is based on a real-time, single-molecule, nano-nitch sequencing technology that can generate very long reads (up to 20-kb) in contrast to the shorter reads produced by the first and second generation sequencing technologies. As a new platform, it is important to assess the sequencing error rate, as well as the quality control (QC) parameters associated with the PacBio sequence data. In this study, a mixture of 10 prior known, closely related DNA amplicons were sequenced using the PacBio RS sequencing platform. After aligning Circular Consensus Sequence (CCS) reads derived from the above sequencing experiment to the known reference sequences, we found that the median error rate was 2.5% without read QC, and improved to 1.3% with an SVM based multi-parameter QC method. In addition, aDe Novoassembly was used as a downstream application to evaluate the effects of different QC approaches. This benchmark study indicates that even though CCS reads are post error-corrected it is still necessary to perform appropriate QC on CCS reads in order to produce successful downstream bioinformatics analytical results.
authors.affiliation: Laboratory of Immunopathogenesis and Bioinformatics, SAIC-Frederick, Inc., Frederick National Laboratory, MD 21702, USA.
authors.forename: Xiaoli
authors.initials: X
authors.lastname: Jiao
authors.forename: Xin
authors.initials: X
authors.lastname: Zheng
authors.forename: Liang
authors.initials: L
authors.lastname: Ma
authors.forename: Geetha
authors.initials: G
authors.lastname: Kutty
authors.forename: Emile
authors.initials: E
authors.lastname: Gogineni
authors.forename: Qiang
authors.initials: Q
authors.lastname: Sun
authors.forename: Brad T
authors.initials: BT
authors.lastname: Sherman
authors.forename: Xiaojun
authors.initials: X
authors.lastname: Hu
authors.forename: Kristine
authors.initials: K
authors.lastname: Jones
authors.forename: Castle
authors.initials: C
authors.lastname: Raley
authors.forename: Bao
authors.initials: B
authors.lastname: Tran
authors.forename: David J
authors.initials: DJ
authors.lastname: Munroe
authors.forename: Robert
authors.initials: R
authors.lastname: Stephens
authors.forename: Dun
authors.initials: D
authors.lastname: Liang
authors.forename: Tomozumi
authors.initials: T
authors.lastname: Imamichi
authors.forename: Joseph A
authors.initials: JA
authors.lastname: Kovacs
authors.forename: Richard A
authors.initials: RA
authors.lastname: Lempicki
authors.forename: Da Wei
authors.initials: DW
authors.lastname: Huang
keywords: CCS read; PacBio; SVM regression; assembly; pass number; quality control (QC); quality value (QV)