Shotgun Metagenomics

There are many different ways to analyze a shotgun metagenome though the quality and amount of data can be the deciding factor on which route to take. For larger, high quality datasets, de novo sequencing is often an option worth entertaining.  For sparse and/or lower quality datasets assembly free methods such as binning or marker gene analysis are the preferred methods.

Sharpton TJ (2014) An introduction to the analysis of shotgun metagenomic data. Front. Plant Sci. 5:209. doi: 10.3389/fpls.2014.00209