The purpose of this project is to analyse a dataset of 16S amplicon sequencing to assess fish biodiversity. Our goal is to run one or more bioinformatics pipelines, perform simple ecological analyses, and compare results. A driving question to this project is: does using different bioinformatics protocols make a difference in the biological conclusions?
Team members
- Cindy Bessey
- Vini Salazar
- ???
Steps:
- Demultiplex Illumina sequencing data (using
obitools/ngsfilter). - Basic preprocessing and length filtering with fastp.
- Create a custom reference database using only fish species from the OBITools reference database (see the Wolves tutorial for more information).
- Run different bioinformatics pipelines.
- Perform simple ecological analyses.
- Compare results of pipelines.
References:
- Berry, Tina E., et al. "DNA metabarcoding for diet analysis and biodiversity: A case study using the endangered Australian sea lion (Neophoca cinerea)." Ecology and Evolution 7.14 (2017): 5435-5453.
- Kumar, Girish, et al. "Comparing eDNA metabarcoding primers for assessing fish communities in a biodiverse estuary." PLoS one 17.6 (2022): e0266720.