I never metagenomics I didn’t like
“Let another man praise thee, and not thine own mouth; a stranger, and not thine own lips.” — Proverbs 27:2
“What-ever” — Me
In PLoS Computational Biology this week, a trio of researchers provides a review of the challenges that metagenomics might ― and already do ― pose for bioinformaticians. The authors refer to metagenomic sequencing data as “noisy and partial.” Their review specifically addresses the computational requirements presented by metagenomics, rather than a comprehensive review of the current technologies. The review concludes with a “representative studies illustrating different facets of recent scientific discoveries made using metagenomics.”
I participated in writing this article for two reasons: first, Phil Bourne, the Editor in Chief of PLoS Computational Biology is a very persuasive fellow (in a good way). Second, one of the mandates of my position at the CAMERA project at the time was to develop new and innovative bioinformatics methods for metagenomics. As I was immersed in the field and the latest professional literature anyway, writing a review seems like a good way to communicate the latest and greatest in the field, both to others but also to ourselves (John, Adam and I, all working in CAMERA). So we decided to write this up. While writing it, this article went through a few drastic alterations: Life Happened to me a couple of times, including changing jobs and a 3,500 km move, which caused a few months of hiatus in the writing. Once we got back to writing, the field changed: new research and new software materialized and at least one software package we were writing about fell off the face of the Earth, so revisions and insertions were necessary. Second, the manuscript started to blow up uncontrollably: there is so much to touch upon in computational metagenomics! Obviously, the field is a moving target but anything we write, especially about software, will be outdated by the time it is published. We therefore decided against the laundry list approach, and focused more on general methods. We also culled a lot of interesting things (sequencing validation, eukaryotic metagenomics) to keep the article relatively brief and flowing.
I hope you like the final result. There’s the comment section in PLoS, you are welcome to make good use of it.
Wooley, J., Godzik, A., & Friedberg, I. (2010). A Primer on Metagenomics PLoS Computational Biology, 6 (2) DOI: 10.1371/journal.pcbi.1000667