[x] - Find MRSA vs MSSA dataset from lab dataset or public dataset that can be compared to visualize large insertions between the assemblies. Downloaded/Processing
[ ] - Run through MRSA/MSSA comparison to verify that things run smoothly (STEPHANIE)
[ ] - Run through VRE/VSE comparison to verify that things run smoothly (Evan)
[ ] - Add Plasmid typer tool run to type plasmids to visualize if the insertion is on plamsid or chrmosome, explore manual.
[ ] - Pick plasmid tool and verify that manual is easy to understand and tool is easy to run. test between mob-suite and plascope
[x] - Get rid of mapping back reads to assembly to show deletion and coverage.
[x] - Loading Prokka annotation files in ACT.
[x] - Change the flow of analysis. Assembly - Abacas - ACT - plasmid typing - Prokka
[ ] - Add Prokka unix challenges to explore various annotation files
[x] - Remove the sections from read mapping to assembly (Ali)