All the code used to analyse the 16S dataset obtained during a wet weather event in Rose Bay in Winter 2019.
References:
Dada2 Pipeline: Callahan, B.J., Mcmurdie, P.J., Rosen, M.J., Han, A.W., Johnson, A.J.A., Holmes, S.P., 2016. DADA2 : High-resolution sample inference from Illumina amplicon data. Nature Methods 13. https://doi.org/10.1038/nmeth.3869
Dixon, P., 2003. Computer program review VEGAN , a package of R functions for community ecology. Journal of Vegetation Science 14, 927–930.
Martin, M., 2011. Cutadapt Removes Adapter Sequences From High-Throughput Sequencing Reads. EMBnet,journal.
Indicator Species: de Caceres, M., Jansen, F., 2018. indicspecies: Relationship between species and groups of sites. R package version 1.7.5.
Source Tracker: Knights, D., Kuczynski, J., Charlson, E.S., Zaneveld, J., Mozer, M.C., Collman, R.G., Bushman, F.D., Knight, R., Kelley, S.T., 2011. Bayesian community-wide culture-independent microbial source tracking. Nature Methods 8, 761–765. https://doi.org/10.1038/nmeth.1650