Journal of Proteomics & Bioinformatics
Open Access

Suzanne M. Garland

Publications

• 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 Tabrizi Erica 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

  Abstract PDF

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