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Article: BASE: a practical de novo assembler for large genomes using long NGS reads

TitleBASE: a practical de novo assembler for large genomes using long NGS reads
Authors
Issue Date2016
PublisherBioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcgenomics/
Citation
BMC Genomics, 2016, v. 17 n. suppl., p. article no. 499 How to Cite?
Abstract© 2016 The Author(s). Background: De novo genome assembly using NGS data remains a computation-intensive task especially for large genomes. In practice, efficiency is often a primary concern and favors using a more efficient assembler like SOAPdenovo2. Yet SOAPdenovo2, based on de Bruijn graph, fails to take full advantage of longer NGS reads (say, 150 bp to 250 bp from Illumina HiSeq and MiSeq). Assemblers that are based on string graphs (e.g., SGA), though less popular and also very slow, are more favorable for longer reads. Methods: This paper shows a new de novo assembler called BASE. It enhances the classic seed-extension approach by indexing the reads efficiently to generate adaptive seeds that have high probability to appear uniquely in the genome. Such seeds form the basis for BASE to build extension trees and then to use reverse validation to remove the branches based on read coverage and paired-end information, resulting in high-quality consensus sequences of reads sharing the seeds. Such consensus sequences are then extended to contigs. Results: Experiments on two bacteria and four human datasets shows the advantage of BASE in both contig quality and speed in dealing with longer reads. In the experiment on bacteria, two datasets with read length of 100 bp and 250 bp were used. Especially for the 250 bp dataset, BASE gives much better quality than SOAPdenovo2 and SGA and is simlilar to SPAdes. Regarding speed, BASE is consistently a few times faster than SPAdes and SGA, but still slower than SOAPdenovo2. BASE and Soapdenov2 are further compared using human datasets with read length 100 bp, 150 bp and 250 bp. BASE shows a higher N50 for all datasets, while the improvement becomes more significant when read length reaches 250 bp. Besides, BASE is more-meory efficent than SOAPdenovo2 when sequencing data with error rate. Conclusions: BASE is a practically efficient tool for constructing contig, with significant improvement in quality for long NGS reads. It is relatively easy to extend BASE to include scaffolding.
Persistent Identifierhttp://hdl.handle.net/10722/235315
ISSN
2015 Impact Factor: 3.867
2015 SCImago Journal Rankings: 2.343

 

DC FieldValueLanguage
dc.contributor.authorLIU, B-
dc.contributor.authorLIU, CM-
dc.contributor.authorLI, D-
dc.contributor.authorLI, Y-
dc.contributor.authorTing, HF-
dc.contributor.authorYiu, SM-
dc.contributor.authorLUO, R-
dc.contributor.authorLam, TW-
dc.date.accessioned2016-10-14T13:52:32Z-
dc.date.available2016-10-14T13:52:32Z-
dc.date.issued2016-
dc.identifier.citationBMC Genomics, 2016, v. 17 n. suppl., p. article no. 499-
dc.identifier.issn1471-2164-
dc.identifier.urihttp://hdl.handle.net/10722/235315-
dc.description.abstract© 2016 The Author(s). Background: De novo genome assembly using NGS data remains a computation-intensive task especially for large genomes. In practice, efficiency is often a primary concern and favors using a more efficient assembler like SOAPdenovo2. Yet SOAPdenovo2, based on de Bruijn graph, fails to take full advantage of longer NGS reads (say, 150 bp to 250 bp from Illumina HiSeq and MiSeq). Assemblers that are based on string graphs (e.g., SGA), though less popular and also very slow, are more favorable for longer reads. Methods: This paper shows a new de novo assembler called BASE. It enhances the classic seed-extension approach by indexing the reads efficiently to generate adaptive seeds that have high probability to appear uniquely in the genome. Such seeds form the basis for BASE to build extension trees and then to use reverse validation to remove the branches based on read coverage and paired-end information, resulting in high-quality consensus sequences of reads sharing the seeds. Such consensus sequences are then extended to contigs. Results: Experiments on two bacteria and four human datasets shows the advantage of BASE in both contig quality and speed in dealing with longer reads. In the experiment on bacteria, two datasets with read length of 100 bp and 250 bp were used. Especially for the 250 bp dataset, BASE gives much better quality than SOAPdenovo2 and SGA and is simlilar to SPAdes. Regarding speed, BASE is consistently a few times faster than SPAdes and SGA, but still slower than SOAPdenovo2. BASE and Soapdenov2 are further compared using human datasets with read length 100 bp, 150 bp and 250 bp. BASE shows a higher N50 for all datasets, while the improvement becomes more significant when read length reaches 250 bp. Besides, BASE is more-meory efficent than SOAPdenovo2 when sequencing data with error rate. Conclusions: BASE is a practically efficient tool for constructing contig, with significant improvement in quality for long NGS reads. It is relatively easy to extend BASE to include scaffolding.-
dc.languageeng-
dc.publisherBioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcgenomics/-
dc.relation.ispartofBMC Genomics-
dc.rightsBMC Genomics. Copyright © BioMed Central Ltd.-
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.-
dc.titleBASE: a practical de novo assembler for large genomes using long NGS reads-
dc.typeArticle-
dc.identifier.emailTing, HF: hfting@cs.hku.hk-
dc.identifier.emailYiu, SM: smyiu@cs.hku.hk-
dc.identifier.emailLam, TW: hresltk@hkucc.hku.hk-
dc.identifier.authorityTing, HF=rp00177-
dc.identifier.authorityYiu, SM=rp00207-
dc.identifier.authorityLam, TW=rp00135-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1186/s12864-016-2829-5-
dc.identifier.pmid27586129-
dc.identifier.scopuseid_2-s2.0-84984679677-
dc.identifier.hkuros269852-
dc.identifier.volume17-
dc.identifier.issuesuppl.-
dc.identifier.spagearticle no. 499-
dc.identifier.epagearticle no. 499-
dc.publisher.placeUnited Kingdom-

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