Author: Sofia Morfopoulou; Vincent Plagnol
Title: Bayesian mixture analysis for metagenomic community profiling. Document date: 2014_7_25
ID: 058r9486_14
Snippet: There are three datasets: simHC, simMC, simLC corresponding to high, medium and low complexity of the metagenomic community respectively. The three methods were applied to simHC, as this is the highest complexity dataset, with many closely related strains with similar abundances and no dominant species. The lowest abundance is 255 reads out of 118,000 reads. The bioinformatics processing in this instance consisted of a BLASTn comparison to all NC.....
Document: There are three datasets: simHC, simMC, simLC corresponding to high, medium and low complexity of the metagenomic community respectively. The three methods were applied to simHC, as this is the highest complexity dataset, with many closely related strains with similar abundances and no dominant species. The lowest abundance is 255 reads out of 118,000 reads. The bioinformatics processing in this instance consisted of a BLASTn comparison to all NCBI bacterial genomes (ftp://ftp.ncbi.nlm.nih.gov/ genomes/Bacteria/all.fna.tar.gz). The number of genomes mapped, retrieved from the the BLASTn output was ∼2,500.
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