2.50
Hdl Handle:
http://hdl.handle.net/10033/615804
Title:
Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data.
Authors:
Frank, J A; Pan, Y; Tooming-Klunderud, A; Eijsink, V G H; McHardy, A C; Nederbragt, A J; Pope, P B
Abstract:
DNA assembly is a core methodological step in metagenomic pipelines used to study the structure and function within microbial communities. Here we investigate the utility of Pacific Biosciences long and high accuracy circular consensus sequencing (CCS) reads for metagenomic projects. We compared the application and performance of both PacBio CCS and Illumina HiSeq data with assembly and taxonomic binning algorithms using metagenomic samples representing a complex microbial community. Eight SMRT cells produced approximately 94 Mb of CCS reads from a biogas reactor microbiome sample that averaged 1319 nt in length and 99.7% accuracy. CCS data assembly generated a comparative number of large contigs greater than 1 kb, to those assembled from a ~190x larger HiSeq dataset (~18 Gb) produced from the same sample (i.e approximately 62% of total contigs). Hybrid assemblies using PacBio CCS and HiSeq contigs produced improvements in assembly statistics, including an increase in the average contig length and number of large contigs. The incorporation of CCS data produced significant enhancements in taxonomic binning and genome reconstruction of two dominant phylotypes, which assembled and binned poorly using HiSeq data alone. Collectively these results illustrate the value of PacBio CCS reads in certain metagenomics applications.
Affiliation:
Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, 1432 Norway.
Citation:
Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data. 2016, 6:25373 Sci Rep
Journal:
Scientific reports
Issue Date:
2016
URI:
http://hdl.handle.net/10033/615804
DOI:
10.1038/srep25373
PubMed ID:
27156482
Type:
Article
Language:
en
ISSN:
2045-2322
Appears in Collections:
publications of the research group bioinformatics in infection research ([BRICS] BIFO)

Full metadata record

DC FieldValue Language
dc.contributor.authorFrank, J Aen
dc.contributor.authorPan, Yen
dc.contributor.authorTooming-Klunderud, Aen
dc.contributor.authorEijsink, V G Hen
dc.contributor.authorMcHardy, A Cen
dc.contributor.authorNederbragt, A Jen
dc.contributor.authorPope, P Ben
dc.date.accessioned2016-07-08T08:44:39Z-
dc.date.available2016-07-08T08:44:39Z-
dc.date.issued2016-
dc.identifier.citationImproved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data. 2016, 6:25373 Sci Repen
dc.identifier.issn2045-2322-
dc.identifier.pmid27156482-
dc.identifier.doi10.1038/srep25373-
dc.identifier.urihttp://hdl.handle.net/10033/615804-
dc.description.abstractDNA assembly is a core methodological step in metagenomic pipelines used to study the structure and function within microbial communities. Here we investigate the utility of Pacific Biosciences long and high accuracy circular consensus sequencing (CCS) reads for metagenomic projects. We compared the application and performance of both PacBio CCS and Illumina HiSeq data with assembly and taxonomic binning algorithms using metagenomic samples representing a complex microbial community. Eight SMRT cells produced approximately 94 Mb of CCS reads from a biogas reactor microbiome sample that averaged 1319 nt in length and 99.7% accuracy. CCS data assembly generated a comparative number of large contigs greater than 1 kb, to those assembled from a ~190x larger HiSeq dataset (~18 Gb) produced from the same sample (i.e approximately 62% of total contigs). Hybrid assemblies using PacBio CCS and HiSeq contigs produced improvements in assembly statistics, including an increase in the average contig length and number of large contigs. The incorporation of CCS data produced significant enhancements in taxonomic binning and genome reconstruction of two dominant phylotypes, which assembled and binned poorly using HiSeq data alone. Collectively these results illustrate the value of PacBio CCS reads in certain metagenomics applications.en
dc.language.isoenen
dc.relationinfo:eu-repo/grantAgreement/EC/FP7/336355en
dc.rightsopenAccessen
dc.rights.urihttp://creativecommons.org/licenses/by-nc-sa/4.0/*
dc.titleImproved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data.en
dc.typeArticleen
dc.contributor.departmentDepartment of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, 1432 Norway.en
dc.identifier.journalScientific reportsen

Related articles on PubMed

This item is licensed under a Creative Commons License
Creative Commons
All Items in HZI are protected by copyright, with all rights reserved, unless otherwise indicated.