Data Science Project 1

Microbial Community Analysis

QIIME2 logo

16S rRNA amplicon sequencing

Data processing and analysis with QIIME 2
This first project will look at samples collected along the Cement Creek, Animas and San Juan rivers within the San Juan Watershed. Using QIIME 2, students will learn about alpha and beta diversity tools, classifiers and other downstream analysis of 16S rRNA amplicon data. We will also give students a short course on the command line using The Carpentries' Unix Shell tutorial. Be prepared for a fun 2-days visualizing data from environmental samples!

Data Science Project 2

Identifying Antibiotic Resistance Genes

Scheme of ARGs

Metals

In acid mine drainage (AMD), heavy metal contamination is harmful to both ecosystem function and human health. Excessive heavy metals in water or soil may impose selective pressure on microbes and change microbial communities. This project will use MinION sequencing to sequence whole genomes to gather information about the presence ARGs. This data analysis will explore Nanopore reads! We will also load samples onto the Nanopore in real-time!
Photo from the paper: Revealing antimicrobial resistance in stormwater with MinION
Another reference paper: Bacterial Heavy-Metal and Antibiotic Resistance Genes in a Copper Tailing Dam Area in Northern China.