Osburn, Ernie

Research Activities

My group will use the HPC system for storage of high-throughput sequence data and bioinformatic analysis of sequence data. We use a number of existing bioinformatic tools to accomplish these goals (more information below).

List of Projects

Growth rates of soil microbiomes across global ecosystems and land management regimes

For this project, we are analyzing soil metagenomes to estimate bacterial growth rates across different ecosystem types and determine how bacterial growth potential varies across environmental variation and in response to different land management practices (e.g., agricultural practices such as tillage).

Computational Methods

The data storage and bioinformatic methods we need should be possible with the resources already available at UK.

List of Software

We use many different kinds of bioinformatic software to accomplish our goals. In general, these tools allow for the quality filtering and various downstream bioinformatic analyses of metagenomic sequence data. Here are some of the software we use: Qiime2, DADA2, Rstudio, python, fastqc, trimmomatic, megahit, metaSPADES, bwa, bbmap, samtools, kraken2, prodigal, blastn, MicrobeCensus, eggNOG mapper, DIAMOND. This is not intended to be an exhaustive list since new needs arise all the time. At prior institutions, I was accustomed to installing software myself on my HPC account if it was not available as a module.