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 #51 would have to be done from this assembly too
lskatz
commented
4 years ago
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
SneakerNet/assemblies/sampleName/spades/