I’m extremely interested in metagenomics - especially assembly and classification. One of the projects I’ve been working on is taxonomic classification of metagenomes using sourmash - a tool for calculation and comparison of Minhash sketches. The authors of the Mash: fast genome and metagenome distance estimation using MinHash demonstrated the utility of minHash sketches for and accurate clustering of genomes and metagenomes. Using their work as inspiration our lab developed sourmash to explore some additional questions we’re interested in. The sbt gather functionality of sourmash compares minHash signatures computed with sourmash to an index containing signatures calculated for all of the microbial genomes in the NCBI RefSeq database. My advisor, C. Titus Brown and Luis Irber, a graduate student in our lab describe method for building the index and its functionality.
Last year I was a participant in the 2014 Next Gen Sequence course at [Kellogg Biological Station] (http://www.kbs.msu.edu/) led by C. Titus Brown. After just two short weeks I left amazed and empowered. We covered a vast array of topics including: cloud computing using [amazon cloud services] (https://aws.amazon.com/), genome assembly, mRNA-seq, experimental design, open science, etc. The instructors brought great energy and made the course accessible to students at all levels. Upon returning to my lab I dove into analyzing my own ngs data and never looked back. This summer I had the pleasure of returning to Kellogg Biological station and beautiful gull lake to TA the [2015 course] (http://angus.readthedocs.org/en/2015/).