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Gene. 2012 Sep 1;505(2):259-65. doi: 10.1016/j.gene.2012.06.014. Epub 2012 Jun 15.

TWARIT: an extremely rapid and efficient approach for phylogenetic classification of metagenomic sequences.

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1
Bio-sciences R&D Division, TCS Innovation Labs, Tata Research Development & Design Centre, 54-B, Hadapsar Industrial Estate, Pune, 411013, India. maheedhar@atc.tcs.com

Abstract

Phylogenetic assignment of individual sequence reads to their respective taxa, referred to as 'taxonomic binning', constitutes a key step of metagenomic analysis. Existing binning methods have limitations either with respect to time or accuracy/specificity of binning. Given these limitations, development of a method that can bin vast amounts of metagenomic sequence data in a rapid, efficient and computationally inexpensive manner can profoundly influence metagenomic analysis in computational resource poor settings. We introduce TWARIT, a hybrid binning algorithm, that employs a combination of short-read alignment and composition-based signature sorting approaches to achieve rapid binning rates without compromising on binning accuracy and specificity. TWARIT is validated with simulated and real-world metagenomes and the results demonstrate significantly lower overall binning times compared to that of existing methods. Furthermore, the binning accuracy and specificity of TWARIT are observed to be comparable/superior to them. A web server implementing TWARIT algorithm is available at http://metagenomics.atc.tcs.com/Twarit/

PMID:
22710135
DOI:
10.1016/j.gene.2012.06.014
[Indexed for MEDLINE]
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