PROJECT TITLE :

Measuring Cluster Stability in a Large Scale Phylogenetic Analysis of Functional Genes in Metagenomes Using pplacer

ABSTRACT:

Analysis of metagenomic sequence knowledge requires a multi-stage workflow. The results of each intermediate step possess an inherent uncertainty and doubtless impact the as-however-unmeasured statistical significance of downstream analyses. Here, we describe our phylogenetic analysis pipeline that uses the pplacer program to position many shotgun sequences resembling a single practical gene onto a fastened phylogenetic tree. We have a tendency to then use the squash clustering methodology to check multiple samples with respect to that gene. We have a tendency to approximate the statistical significance of each gene's clustering result by measuring its cluster stability, the consistency of that clustering result when the probabilistic placements made by pplacer are systematically reassigned and then clustered once more, as measured by the adjusted Rand Index. We have a tendency to realize that among the genes investigated, the majority of analyses are stable, based on the common adjusted Rand Index. We investigated properties of every gene that will explain less stable results. These genes tended to possess less convex reference trees, less total reads recruited to the gene, and a greater Expected Distance between Placement Locations as given by pplacer when examined in combination. However, for a private purposeful gene, these measures alone do not predict cluster stability.