Binning metagenomic contigs by coverage and composition

• Published in: Nature methods Vol. 11; no. 11; pp. 1144 - 1146
• Main Authors: Alneberg, Johannes, Bjarnason, Brynjar Smári, de Bruijn, Ino, Schirmer, Melanie, Quick, Joshua, Ijaz, Umer Z, Lahti, Leo, Loman, Nicholas J, Andersson, Anders F, Quince, Christopher
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.11.2014; Nature Publishing Group
• Subjects: 45/22; 45/23; 631/114/1305; 631/114/2785; 631/208/212/2142; 631/326/2565/2142; Algorithms; Bifidobacterium - genetics; Bioinformatics; Biological Microscopy; Biological Techniques; Biomedical Engineering/Biotechnology; Biotechnology; brief-communication; Computational biology; Contig Mapping - methods; DNA sequencing; Escherichia coli K12 - genetics; Feces - microbiology; Gastrointestinal Tract - microbiology; Genetic research; Genome, Bacterial - genetics; Genomes; Genomics; Humans; Innovations; Life Sciences; Metagenome - genetics; Metagenomics - methods; Microbial activity; Microbiology; Microbiota - genetics; Nucleotide sequencing; Proteomics; Sequence Analysis, DNA - methods; Sequences; Shiga-Toxigenic Escherichia coli - genetics; Software
• ISSN: 1548-7091; 1548-7105; 1548-7105
• DOI: 10.1038/nmeth.3103

The CONCOCT software performs unsupervised binning of metagenomic contigs across multiple samples to allow better genome reconstruction from microbial communities. 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.