SPAdes assembly

[lskatz]

Is your feature request related to a problem? Please describe.
For some things like AMR, a skesa assembly will not work because it removes repeat elements,
which are often AMR related.

Describe the solution you'd like
We want to have a SPAdes-based assembly when genomes are assembled

Describe alternatives you've considered
N/A

Additional context
This would put SneakerNet AMR in sync with the rest of NARMS on how AMR determinant genes are detected

• One idea is to put the assemblies into SneakerNet/assemblies/sampleName/spades/
• Would need to document the new assemblies in the assembleAll.pl plugin
• Would want to pull assemblies from this new location into the staramr plugin
• plasmid typing from Plasmid plugin #51 would have to be done from this assembly too

[lskatz]

Point of contact @jchen232