Review papers on the topic of metagenomics
Edit (01/13): A special issue in Briefings in Bioinformatics: Bioinformatics approaches and tools for metagenomic analysis (Novermber 2012)
A primer on metagenomics (2011) in PLoS Computational Biology. Presents a higher level overview of the methods and provides definitions and formulas for the most commonly used metrics and quantities such as metagenome coverage and diversity estimation. Multiple computational approaches are presented.
- Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies (Dec 2011) in PLoS ONE. This is a paper by the authors of the mothur package. They describe the trials and tribulations of those attempting to make sense of the error prone data that comes potentially from tens of thousands of similar genomes. A must read for everyone working in this field.
Analysis using mothur
- Introducing mothur: open-source software for describing and comparing microbial communities (2009) in Appl Environ Microbiol.
Analysis using QIIME
- Using QIIME to analyze 16S rRNA gene sequences from microbial communities (2011). in Curr Protoc Bioinformatics
- QIIME allows analysis of high-throughput community sequencing data (2010). in Nat Methods
Analysis using MEGAN
- Analysis of 16S rRNA environmental sequences using MEGAN (2011) in BMC Genomics
- Introduction to the analysis of environmental sequences: metagenomics with MEGAN (2012) in Methods Mol Biol.
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