GPSC assignment

Install PopPUNK 2.4 as per instructions at PopPUNK documentation and download 
the GPS reference database and the GPS designation.

Files required to run GPSC assignment using PopPUNK 2.4:
1. A 2-column tab-delimited file containing sample name and path to the
   corresponding assembly (no header)
2. GPS reference database <GPS_v6>
3. GPS designation <GPS_v6_external_clusters.csv>

output directory name is assigned using --output
number of threads can be changed using –threads

Run GPSC assignment:

poppunk_assign --db GPS_v6 \
               --distances GPS_v6/GPS_v6.dists \
               --query <2-column path to assembly> \
               --output <GPSC_assignment> \
               --external-clustering \
               GPS_v6_external_clusters.csv
               
Outputs:

_clusters.csv: popPUNK clusters with dataset specific nomenclature
_external_clusters.csv: GPSC v6 scheme designations

Novel Clusters are assigned NA in the _external_clusters.csv as they have 
not been defined in the v6 dataset used to designate the GPSCs. Please email: 
globalpneumoseq@gmail.com to have novel clusters added to the database and a 
GPSC cluster name assigned after you have checked for low level contamination 
which may contribute to biased accessory distances.

Merged clusters: Unsampled diversity may represent missing variation linking two 
clusters. GPSCs are then merged. For example if GPSC23 and GPSC362 merged, the 
GPSC would be then reported as GPSC23, with a merge history of GPSC23;362.