Mihai Pop

From STAMPS

I am a computer scientist working on applications of computers to the analysis of biological data. My work is mostly focused on the development of alignment and assembly algorithms and I am particularly interested in metagenomics applications.

In this year's course I'm covering both taxonomic annotation and metagenomic assembly - topics that at a first glance seem unrelated. They are, however, two sides of a same coin. One of the main goals we have when analyzing microbial communities is to figure out who is there and what they do. Taxonomic annotation of sequences (either 16S or whole shotgun) provides a guess at answering the question. Assembling the actual genomes provides an even better guess as now you can identify specific functions that might distinguish otherwise identical genomes.

Taxonomic annotation

The slides of my talk are available here: File:Metagenomic taxonomic assignment.pdf

The talk is broad, focusing on taxonomic annotation irrespective of "substrate" (marker genes or random read). I cannot give you specific recommendations about software to use, though I provide some examples. My goal is to give you an overview of the different ways one can use to tackle this problem, allowing you to make the decision about the most appropriate approach for your data.

Metagenomic assembly

This year there will be no hands-on demonstration (which is hard to do for assembly anyway) but you can access last year's data here:

/class/stamps-shared/Metamos-demo

Also, after the course you can get the data here (no login required): http://gembox.cbcb.umd.edu/stamps2017/Assembly_demo.zip

Theory slides - File:Metagenomics theory.pdf - A video of part of this presentation (with the animations missing from the PDF) is available here

Course materials for practical part (something you can do on your own): http://stamps.mbl.edu/index.php/Hands-on_with_assembly


Some additional information

Tools for visualizing assembly graphs