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arXiv · 1312.4038

CONCOCT: Clustering cONtigs on COverage and ComposiTion

Johannes Alneberg·Brynjar Smari Bjarnason·Ino de Bruijn·Melanie Schirmer·Joshua Quick·Umer Z. Ijaz·Nicholas J. Loman·Anders F. Andersson·Christopher Quince
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Abstract

Metagenomics enables the reconstruction of microbial genomes in complex microbial communities without the need for culturing. Since assembly typically results in fragmented genomes the grouping of genome fragments (contigs) belonging to the same genome, a process referred to as binning, remains a major informatics challenge. Here we present CONCOCT, a computer program that combines three types of information - sequence composition, coverage across multiple sample, and read-pair linkage - to automatically bin contigs into genomes. We demonstrate high recall and precision rates of the program on artificial as well as real human gut metagenome datasets.

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Johannes Alneberg, Brynjar Smari Bjarnason, Ino de Bruijn, Melanie Schirmer, Joshua Quick, Umer Z. Ijaz, Nicholas J. Loman, Anders F. Andersson, Christopher Quince. 2013-12-14. CONCOCT: Clustering cONtigs on COverage and ComposiTion. https://arxiv.org/abs/1312.4038

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