Journal of Proteomics & Bioinformatics
Open Access
ISSN: 0974-276X
ISSN: 0974-276X
Erica Plummer
Murdoch Childrens Research Institute, The Royal Children’s Hospital, Flemington Rd, Parkville,
Victoria 3052
Australia
Research Article
A Comparison of Three Bioinformatics Pipelines for the Analysis of Preterm Gut Microbiota using 16S rRNA Gene Sequencing Data
Author(s): Erica Plummer, Jimmy Twin, Dieter M. Bulach, Suzanne M. Garland and Sepehr N TabriziErica Plummer, Jimmy Twin, Dieter M. Bulach, Suzanne M. Garland and Sepehr N Tabrizi
Objective and Methods: Analysis of massive parallel sequencing 16S rRNA data requires the use of sophisticated bioinformatics pipelines. Several pipelines are available, however there is limited literature available comparing the features, advantages and disadvantages of each pipeline. This makes the choice of which method to use often unclear. Using gut microbial read data collected from a cohort of very preterm babies, we compared three pipelines commonly used for 16S rRNA gene analysis: MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST), Quantitative Insights into Microbial Ecology (QIIME) and mothur. Using primarily default parameters, the three pipelines were compared in terms of taxonomic classification, diversity analysis and usability.
Results: Overall, the three pipelines detected the same phylum in similar abundances (P>0.05). A difference was obse.. View More»
DOI:
10.4172/jpb.1000381