Technological advances in next-generation sequencing-based approaches have greatly impacted the analysis of microbial community composition. In particular, 16S rRNA-based methods have been widely used to analyze the whole set of bacteria present in a target environment. As a consequence, several specific bioinformatic pipelines have been developed to manage these data.MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST) and Quantitative Insights IntoMicrobial Ecology (QIIME) are two freely available tools for metagenomic analyses that have been used in a wide range of studies. Here, we report the comparative analysis of the same dataset with both QIIME and MG-RAST in order to evaluate their accuracy in taxonomic assignment and in diversity analysis.We found that taxonomic assignment was more accurate with QIIME which, at family level, assigned a significantly higher number of reads.Thus, QIIME generated a more accurate BIOM file, which in turn improved the diversity analysis output. Finally, although informatics skills are needed to install QIIME, it offers a wide range of metrics that are useful for downstream applications and, not less important, it is not dependent on server times.

Comparative metagenomic analysis of human gut microbiome composition using two different bioinformatic pipelines / D'Argenio, Valeria; Casaburi, Giorgio; Precone, Vincenza; Salvatore, Francesco. - In: BIOMED RESEARCH INTERNATIONAL. - ISSN 2314-6133. - 2014:(2014), pp. 1-10. [10.1155/2014/325340]

Comparative metagenomic analysis of human gut microbiome composition using two different bioinformatic pipelines

D'ARGENIO, VALERIA;CASABURI, GIORGIO;SALVATORE, FRANCESCO
2014

Abstract

Technological advances in next-generation sequencing-based approaches have greatly impacted the analysis of microbial community composition. In particular, 16S rRNA-based methods have been widely used to analyze the whole set of bacteria present in a target environment. As a consequence, several specific bioinformatic pipelines have been developed to manage these data.MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST) and Quantitative Insights IntoMicrobial Ecology (QIIME) are two freely available tools for metagenomic analyses that have been used in a wide range of studies. Here, we report the comparative analysis of the same dataset with both QIIME and MG-RAST in order to evaluate their accuracy in taxonomic assignment and in diversity analysis.We found that taxonomic assignment was more accurate with QIIME which, at family level, assigned a significantly higher number of reads.Thus, QIIME generated a more accurate BIOM file, which in turn improved the diversity analysis output. Finally, although informatics skills are needed to install QIIME, it offers a wide range of metrics that are useful for downstream applications and, not less important, it is not dependent on server times.
2014
Comparative metagenomic analysis of human gut microbiome composition using two different bioinformatic pipelines / D'Argenio, Valeria; Casaburi, Giorgio; Precone, Vincenza; Salvatore, Francesco. - In: BIOMED RESEARCH INTERNATIONAL. - ISSN 2314-6133. - 2014:(2014), pp. 1-10. [10.1155/2014/325340]
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11588/621026
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