Evaluation of hybrid and non-hybrid methods for de novo assembly of nanopore reads

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Evaluation of hybrid and non-hybrid methods for de novo assembly of nanopore reads
Title:
Evaluation of hybrid and non-hybrid methods for de novo assembly of nanopore reads
Journal Title:
Bioinformatics
Keywords:
Publication Date:
09 May 2016
Citation:
Ivan Sović, Krešimir Križanović, Karolj Skala, Mile Šikić; Evaluation of hybrid and non-hybrid methods for de novo assembly of nanopore reads , Bioinformatics, Volume 32, Issue 17, 1 September 2016, Pages 2582–2589, https://doi.org/10.1093/bioinformatics/btw237
Abstract:
MOTIVATION: Recent emergence of nanopore sequencing technology set a challenge for established assembly methods. In this work, we assessed how existing hybrid and non-hybrid de novo assembly methods perform on long and error prone nanopore reads. RESULTS: We benchmarked five non-hybrid (in terms of both error correction and scaffolding) assembly pipelines as well as two hybrid assemblers which use third generation sequencing data to scaffold Illumina assemblies. Tests were performed on several publicly available MinION and Illumina datasets of Escherichia coli K-12, using several sequencing coverages of nanopore data (20×, 30×, 40× and 50×). We attempted to assess the assembly quality at each of these coverages, in order to estimate the requirements for closed bacterial genome assembly. For the purpose of the benchmark, an extensible genome assembly benchmarking framework was developed. Results show that hybrid methods are highly dependent on the quality of NGS data, but much less on the quality and coverage of nanopore data and perform relatively well on lower nanopore coverages. All non-hybrid methods correctly assemble the E. coli genome when coverage is above 40×, even the non-hybrid method tailored for Pacific Biosciences reads. While it requires higher coverage compared to a method designed particularly for nanopore reads, its running time is significantly lower.
License type:
PublisherCopyrights
Funding Info:
This work has been supported in part by Croatian Science Foundation under the project UIP-11-2013-7353 ‘Algorithms for Genome Sequence Analysis’. I.S. is supported in part 25 by the Croatian Academy of Sciences and Arts under the project ‘Methods for alignment and assembly of DNA sequences using nanopore sequencing data’.
Description:
Full paper can be downloaded from the Publisher's URL provided.
ISSN:
1367-4803
1460-2059
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