[x] - Choose K. pneumo genomes for BLAST, ARIBA & MLST (ZENA) Holt et al. (2015) PNAS, Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health.
[x] - Assemble the K. pneumo genomes
[x] - Make a metadata file by subsetting the supplement file (ZENA)
[x] - Change to pheatmap (plot AMR genes with origin) (ZENA)
[x] - Explore Ariba all report: (Zena)
[x] - Add exercise to run MLST and overlay on heatmap (ZENA)
[ ] - Decide what genome comparison to do for A. baumanii (Evan)
[ ] - Fraction of genomes that are putative phage?
[ ] - What genes are in genomic rearrangements?
[ ] - Add solution section to the questions asked.
[x] - Change the Blast exercise to finding KPC gene from KPC dataset.
[ ] - Ask to run Ariba MLST step on 5-6 samples. Time this exercise.