OTUreporter: a modular automated pipeline for the analysis and report of amplicon data

While 16S rRNA gene amplicon sequencing is not considered a state-of-the-art technique any more, it is now considered a well-matured technique for the routine screening of samples of microbiological interest. The maturity of the technique with the lower costs, have provided an increased demand even in areas foreign to typical research.

OTUreporter was developed aiming to bridge the gap between a sequencing service provider without dedicated bioinformatics personnel, and a non-expert customer. OTUreporter was also designed keeping in mind customers with limited computing resources for the initial stages of the amplicon data analysis.

Unlike many automated 16S rRNA gene amplicon tools such those made available by sequencing companies (e.g. Illumina's "16S Metagenomics" tool), OTUreporter is not a "black box" and uses software that it is actually used in research context for this matters.

OTUreporter accesses BaseSpace directly to gather amplicon data and sequencing run details, avoiding any need for the manual download. The main program used in the background is mothur. OTUreporter uses a slightly modified version of the MiSeqSOP protocol for processing the amplicon data.

The final output of OTUreporter is a report. The report summarises the details, not only of the analysis, but also of the sequencing jobs themselves. The report, based on a RMarkdown template, creates two different outputs of the same report: a slimmer printer-friendly pdf document, and an extended html output with interactive content.

OTUreporter is currently in beta testing at the Ramaciotti Centre for Genomics.

If you use OTUreporter or reuse any of its contents, please cite the repository at Bitbucket (https://bitbucket.org/xvazquezc/otureporter) or this poster as:
Vázquez-Campos, X., Chilton, A., Koval, J., Tree, J. J., & Wilkins, M. R. OTUreporter: a modular automated pipeline for the analysis and report of amplicon data. Sydney Bioinformatics Research Symposium 2018. 15 Jun 2018. Sydney, NSW, Australia. DOI: 10.6084/m9.figshare.6521171.