title: Web Resources for Metagenomics Studies.
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.
authors.affiliation: Department of Biosciences, Veer Narmad South Gujarat University, Surat 395007, India. Electronic address: dudhagarapr@gmail.com.
authors.forename: Pravin
authors.initials: P
authors.lastname: Dudhagara
authors.affiliation: Department of Biosciences, Veer Narmad South Gujarat University, Surat 395007, India.
authors.forename: Sunil
authors.initials: S
authors.lastname: Bhavsar
authors.affiliation: Department of Biosciences, Veer Narmad South Gujarat University, Surat 395007, India.
authors.forename: Chintan
authors.initials: C
authors.lastname: Bhagat
authors.affiliation: Department of Microbiology, Shree Ramkrishna Institute of Computer Education and Applied Sciences, Surat 395001, India.
authors.forename: Anjana
authors.initials: A
authors.lastname: Ghelani
authors.affiliation: Department of Life Sciences, Hemchandracharya North Gujarat University, Patan 384265, India.
authors.forename: Shreyas
authors.initials: S
authors.lastname: Bhatt
authors.affiliation: Department of Life Sciences, Hemchandracharya North Gujarat University, Patan 384265, India.
authors.forename: Rajesh
authors.initials: R
authors.lastname: Patel
mesh_terms: D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D016247:Information Storage and Retrieval; D020407:Internet; D054892:Metagenome / Q000235:genetics; D056186:Metagenomics / Q000379:methods*; D012984:Software
keywords: Metagenomes; Metagenomics; Software tools; Synthetic metagenome; Web resources