MetaPalette and Bracken

This week, we mostly discussed MetaPalette. Though it can be tricky to install correctly, and I for one have had problems with memory limits, I like it because it pulls genomes from NCBI databases including Bacteria, Archaea, Viruses and Eukaryotes, which is rare in an annotation software workflow.  I also like the fact that it relies on kmers of two sizes (30 and 50) and assigns based on the lowest common ancestor.  A suggestion we posited was to run the program in a virtual server environment.

We also briefly discussed Bracken, which takes adjusts results from Kraken using genome size and Bayesian statistics. The product is a table that includes the original associated numbers, the adjusted reads, and the final percentages.  Matt described an experiment investigating viral reads horse cells.  A custom database worked well here, classifying about 60% of the reads of interest.