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.


Later this month: taxonomic annotation

Just a heads up: in a couple of weeks, August 19th, we’ll talk about Metapalette, Discribinate, and Bracken to continue our discussion of annotation tools without interrupting our thoughts on workflows too much.  I’m currently attempting to use Metapalette, Chris has used Discribinate, and we’re all curious about Bracken.