Metagenomics for Greener Production and
Extraction of Hydrocarbon Energy
Written by Xiaoli Dong
Project Title : Metagenomics for greener production and extraction
of hydrocarbon energy
Project Leader: Gerrit Voordouw
The Genome Canada Bioinformatics provides the following services to the
HMP project: (http://www.hydrocarbonmetagenomics.com)
- Sequence data and metadata database development and maintaining
- Sequence assembly and analysis
- Submission of data to public databases
The BIP has developed an integrated SSU rRNA data analysis pipeline
named Phoenix to analyze the SSU rRNA sequence data from environmental
16S amplicon pyrosequencing. The pipeline uses a number of statistical
tools and software packages. Mothur is used to assign the SSU sequences
which passed the quality control process to operational taxonomic
units (OTUs) based on a distance matrix and calculate the
collector's curves for observed OTUs, the Chao1, ACE richness
estimators, and Shannon's and Simpson's diversity indices. The Unifrac
and Fast Unifrac are used to evaluate the differences among the sampled
communities. The local developed algorithms are used to categorize SSU
rRNA sequences into the higher-oder taxonomy. The pipeline also
provides Megan, dendroscope compatible input files to do the
phylogenetic tree visualization. The BIP is also responsible to
the metagenomics data assembly, annotation, taxonomic binnin