Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data.
Cast your vote
You can rate an item by clicking the amount of stars they wish to award to this item.
When enough users have cast their vote on this item, the average rating will also be shown.
Your vote was cast
Thank you for your feedback
Thank you for your feedback
MetadataShow full item record
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.
CitationImproved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data. 2016, 6:25373 Sci Rep
AffiliationDepartment of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, 1432 Norway.
The following license files are associated with this item:
- MetaCluster-TA: taxonomic annotation for metagenomic data based on assembly-assisted binning.
- Authors: Wang Y, Leung H, Yiu S, Chin F
- Issue date: 2014
- An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome.
- Authors: Ferrarini M, Moretto M, Ward JA, Šurbanovski N, Stevanović V, Giongo L, Viola R, Cavalieri D, Velasco R, Cestaro A, Sargent DJ
- Issue date: 2013 Oct 1
- Unsupervised Binning of Metagenomic Assembled Contigs Using Improved Fuzzy C-Means Method.
- Authors: Liu Y, Hou T, Kang B, Liu F
- Issue date: 2017 Nov-Dec
- Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes.
- Authors: Papudeshi B, Haggerty JM, Doane M, Morris MM, Walsh K, Beattie DT, Pande D, Zaeri P, Silva GGZ, Thompson F, Edwards RA, Dinsdale EA
- Issue date: 2017 Nov 28
- Fragmentation and Coverage Variation in Viral Metagenome Assemblies, and Their Effect in Diversity Calculations.
- Authors: García-López R, Vázquez-Castellanos JF, Moya A
- Issue date: 2015