1. Summary

One of the most exciting bioinformatics advances from the past few years has been our new ability to disentangle microbial genomes from environmental samples called metagenomes. This has allowed us to study the full diversity of life without needing to culture these microbes-- and 99% of microbes have not yet been cultivated. Our ability to "bin" genomes from metagenomes has revolutionized our view of the tree of life, and changed our understanding of our own place within that tree of life. We'll learn how to bin genomes from metagenomes, and by the end of the module you'll have some genomes of your own to explore and play with.

2. Presentation Materials

Click here for the presentation materials.

3. Hands-on Exercise(s)

Click here.

4. Associated Materials/Files

Associated data files are here.

5. Program/Software requirements

Anvi'o: http://merenlab.org/software/anvio/

6. Advanced Material

This paper describes the software used in this module: https://peerj.com/articles/1319/?td=bl

This paper uses bins to change our view of the tree of life: https://www.nature.com/articles/nmicrobiol201648/

This paper changed our view of our place in the tree of life using genomes that had been binned from metagenomes: https://www.nature.com/articles/nature14447?rel=mas

7. Instructor Notes

This module assumes that students know how to:

1. use the Terminal
2. assemble reads into contigs
3. map reads to contigs

Anvi'o has a great website with awesome tutorials: http://merenlab.org/software/anvio/