Binning metagenomic contigs by coverage and composition

Johannes Alneberg; Brynjar Smári Bjarnason; Ino de Bruijn; Melanie Schirmer; Joshua Quick; Umer Z Ijaz; Leo Lahti; Nicholas J Loman; Anders F Andersson; Christopher Quince

doi:10.1038/nmeth.3103

Binning metagenomic contigs by coverage and composition

Johannes Alneberg, Brynjar Smári Bjarnason, Ino de Bruijn, Melanie Schirmer, Joshua Quick, Umer Z Ijaz, Leo Lahti, Nicholas J Loman, Anders F Andersson, Christopher Quince

Biosciences

Research output: Contribution to journal › Article › peer-review

540 Citations (Scopus)

Abstract

Shotgun sequencing enables the reconstruction of genomes from complex microbial communities, but because assembly does not reconstruct entire genomes, it is necessary to bin genome fragments. Here we present CONCOCT, a new algorithm that combines sequence composition and coverage across multiple samples, to automatically cluster contigs into genomes. We demonstrate high recall and precision on artificial as well as real human gut metagenome data sets.

Original language	English
Pages (from-to)	1144-6
Number of pages	3
Journal	Nature Methods
Volume	11
Issue number	11
DOIs	https://doi.org/10.1038/nmeth.3103
Publication status	Published - Nov 2014

Keywords

Algorithms
Bifidobacterium
Contig Mapping
Escherichia coli K12
Feces
Gastrointestinal Tract
Genome, Bacterial
Humans
Metagenome
Metagenomics
Microbiota
Sequence Analysis, DNA
Shiga-Toxigenic Escherichia coli
Software

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10.1038/nmeth.3103

Development of robust analytical pipelines for the analysis of microbial community data from clinical samples
Loman, N.
Medical Research Council
1/09/12 → 31/08/15
Project: Research Councils

Cite this

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title = "Binning metagenomic contigs by coverage and composition",

abstract = "Shotgun sequencing enables the reconstruction of genomes from complex microbial communities, but because assembly does not reconstruct entire genomes, it is necessary to bin genome fragments. Here we present CONCOCT, a new algorithm that combines sequence composition and coverage across multiple samples, to automatically cluster contigs into genomes. We demonstrate high recall and precision on artificial as well as real human gut metagenome data sets.",

keywords = "Algorithms, Bifidobacterium, Contig Mapping, Escherichia coli K12, Feces, Gastrointestinal Tract, Genome, Bacterial, Humans, Metagenome, Metagenomics, Microbiota, Sequence Analysis, DNA, Shiga-Toxigenic Escherichia coli, Software",

author = "Johannes Alneberg and Bjarnason, {Brynjar Sm{\'a}ri} and {de Bruijn}, Ino and Melanie Schirmer and Joshua Quick and Ijaz, {Umer Z} and Leo Lahti and Loman, {Nicholas J} and Andersson, {Anders F} and Christopher Quince",

year = "2014",

month = nov,

doi = "10.1038/nmeth.3103",

language = "English",

volume = "11",

pages = "1144--6",

journal = "Nature Methods",

issn = "1548-7091",

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T1 - Binning metagenomic contigs by coverage and composition

AU - Alneberg, Johannes

AU - Bjarnason, Brynjar Smári

AU - de Bruijn, Ino

AU - Schirmer, Melanie

AU - Quick, Joshua

AU - Ijaz, Umer Z

AU - Lahti, Leo

AU - Loman, Nicholas J

AU - Andersson, Anders F

AU - Quince, Christopher

PY - 2014/11

Y1 - 2014/11

N2 - Shotgun sequencing enables the reconstruction of genomes from complex microbial communities, but because assembly does not reconstruct entire genomes, it is necessary to bin genome fragments. Here we present CONCOCT, a new algorithm that combines sequence composition and coverage across multiple samples, to automatically cluster contigs into genomes. We demonstrate high recall and precision on artificial as well as real human gut metagenome data sets.

AB - Shotgun sequencing enables the reconstruction of genomes from complex microbial communities, but because assembly does not reconstruct entire genomes, it is necessary to bin genome fragments. Here we present CONCOCT, a new algorithm that combines sequence composition and coverage across multiple samples, to automatically cluster contigs into genomes. We demonstrate high recall and precision on artificial as well as real human gut metagenome data sets.

KW - Algorithms

KW - Bifidobacterium

KW - Contig Mapping

KW - Escherichia coli K12

KW - Feces

KW - Gastrointestinal Tract

KW - Genome, Bacterial

KW - Humans

KW - Metagenome

KW - Metagenomics

KW - Microbiota

KW - Sequence Analysis, DNA

KW - Shiga-Toxigenic Escherichia coli

KW - Software

U2 - 10.1038/nmeth.3103

DO - 10.1038/nmeth.3103

M3 - Article

C2 - 25218180

SN - 1548-7091

VL - 11

SP - 1144

EP - 1146

JO - Nature Methods

JF - Nature Methods

IS - 11

ER -

Binning metagenomic contigs by coverage and composition

Abstract

Keywords

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Projects

Development of robust analytical pipelines for the analysis of microbial community data from clinical samples

Cite this