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Review
. 2015 Oct;13(5):296-303.
doi: 10.1016/j.gpb.2015.10.003. Epub 2015 Nov 18.

Web Resources for Metagenomics Studies

Pravin Dudhagara  1 , Sunil Bhavsar  2 , Chintan Bhagat  2 , Anjana Ghelani  3 , Shreyas Bhatt  4 , Rajesh Patel  4
Affiliations
Review

Web Resources for Metagenomics Studies

Pravin Dudhagara et al. Genomics Proteomics Bioinformatics. 2015 Oct.

Abstract

The development of next-generation sequencing (NGS) platforms spawned an enormous volume of data. This explosion in data has unearthed new scalability challenges for existing bioinformatics tools. The analysis of metagenomic sequences using bioinformatics pipelines is complicated by the substantial complexity of these data. In this article, we review several commonly-used online tools for metagenomics data analysis with respect to their quality and detail of analysis using simulated metagenomics data. There are at least a dozen such software tools presently available in the public domain. Among them, MGRAST, IMG/M, and METAVIR are the most well-known tools according to the number of citations by peer-reviewed scientific media up to mid-2015. Here, we describe 12 online tools with respect to their web link, annotation pipelines, clustering methods, online user support, and availability of data storage. We have also done the rating for each tool to screen more potential and preferential tools and evaluated five best tools using synthetic metagenome. The article comprehensively deals with the contemporary problems and the prospects of metagenomics from a bioinformatics viewpoint.

Keywords: Metagenomes; Metagenomics; Software tools; Synthetic metagenome; Web resources.

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Figures

Figure 1
Figure 1
Relative citation of the metagenomics software tools from articles published in peer-reviewed scientific journals by October 2015 Year in the bracket in the legend box indicates the year of original release of the respective tool. Citation of each tool was tracked from Google Scholar. Total citation of all tools is considered as 100% in each year and relative percentage of citations of each tool per year was calculated in relative to the total citations of all tools in the respective year.
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