City co-assembly amr annotation

[aapashkov]

City-level co-assemblies have been finished, and can be found in Alnitak: /data/camda2023/us-cities/assemblies/*.fasta.

It should be annotated with CARD and BLAST.

[nselem]

[ ] Kraken needs to be run first and then extraction commands over the coassemblies [ ] Assembling in needed in extracted reads

[aapashkov]

City co-assembly, taxonomic classification, extraction, and CARD annotation has been finished. The documentation has been uplodad to GitHub here. The counts and presence-absence tables are also available.