OTUreporter

OTUreporter generates standardized reports from MiSeq amplicon sequencing by retrieving BaseSpace amplicon files and sequencing run metadata and processing them with a modified MiSeqSOP implemented in mothur to support microbial community analysis.

Key Features:

• BaseSpace integration: Automatically retrieves amplicon data and sequencing run details from BaseSpace.
• Mothur MiSeqSOP implementation: Processes data using a modified version of the MiSeqSOP protocol implemented in mothur.
• Report generation: Produces a detailed analysis report summarizing the analysis and sequencing job information using an RMarkdown template.
• Output formats: Exports a printer-friendly PDF and an extended HTML version with interactive content.

Scientific Applications:

• Microbial community analysis: Supports mothur-based analyses for microbial community composition and diversity from amplicon datasets.
• Amplicon sequencing run reporting: Provides consolidated reporting of amplicon sequencing results and associated run metadata.

Methodology:

Automatically retrieve amplicon data and sequencing run details from BaseSpace, process data using a modified MiSeqSOP protocol implemented in mothur, and generate reports via an RMarkdown template with PDF and extended HTML outputs.