Multiplexed highly-accurate DNA sequencing of closely-related HIV-1 variants using continuous long reads from single molecule, real-time sequencing

Single Molecule, Real-Time (SMRT) Sequencing (Pacific Biosciences, Menlo Park, CA, USA) provides the longest continuous DNA sequencing reads currently available. However, the relatively high error rate in the raw read data requires novel analysis methods to deconvolute sequences derived from complex...

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Bibliographic Details
Published in:Nucleic acids research 2015-11, Vol.43 (20), p.e129-e129
Main Authors: Dilernia, Dario A, Chien, Jung-Ting, Monaco, Daniela C, Brown, Michael P S, Ende, Zachary, Deymier, Martin J, Yue, Ling, Paxinos, Ellen E, Allen, Susan, Tirado-Ramos, Alfredo, Hunter, Eric
Format: Article
Language:English
Subjects:
Algorithms
Cluster Analysis
Genetic Variation
Genome, Viral
High-Throughput Nucleotide Sequencing - methods
HIV-1 - genetics
Humans
Methods Online
Sequence Alignment
Sequence Analysis, DNA - methods
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Summary:Single Molecule, Real-Time (SMRT) Sequencing (Pacific Biosciences, Menlo Park, CA, USA) provides the longest continuous DNA sequencing reads currently available. However, the relatively high error rate in the raw read data requires novel analysis methods to deconvolute sequences derived from complex samples. Here, we present a workflow of novel computer algorithms able to reconstruct viral variant genomes present in mixtures with an accuracy of >QV50. This approach relies exclusively on Continuous Long Reads (CLR), which are the raw reads generated during SMRT Sequencing. We successfully implement this workflow for simultaneous sequencing of mixtures containing up to forty different >9 kb HIV-1 full genomes. This was achieved using a single SMRT Cell for each mixture and desktop computing power. This novel approach opens the possibility of solving complex sequencing tasks that currently lack a solution.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkv630