GPSC_README_PopPUNK2.txt

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.