Time-Series Analyses of Population Dynamics of an Engineered Bioreactor Ecosystem at Multiple Scales of Resolution
This repository contains executables, submit files, and scripts for analyzing time-series data at multiple scales of resolution (16S rRNA amplicon, qPCR, genome-resolved metagenomics) of an engineered enrichment bioreactor simulating EBPR operating from 2005-2013 at the University of Wisconsin - Madison. The time-series and analyses specifically focus on operation from 2010-2013 as this was a stable period of operation for the R1 reactor.
Raw data and results files including 16S OTU and taxonomy tables, qPCR results, sample extraction sheets, and chemical metadata are in the R1 Bioreactor Figshare Project Repository
Raw sequencing files such as 16S rRNA amplicon sequencing fastq files, shotgun metagenomic sequencing fastq files, and non-redundant metagenome-assembled genome FASTAs are available on NCBI at the Bioproject Accession PRJNA881607.