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GPSC_README.rtf
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{\rtf1\ansi\ansicpg1252\cocoartf1504\cocoasubrtf830
{\fonttbl\f0\froman\fcharset0 TimesNewRomanPSMT;\f1\froman\fcharset0 Times-Roman;}
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\f0\fs32 \cf2 \expnd0\expndtw0\kerning0
\outl0\strokewidth0 \strokec2 Assigning your own data to GPSCs
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\f0\fs32 Install popPUNK as per instructions at https://poppunk.readthedocs.io/en/latest/installation.html and downloaded the GPS reference database \'93GPS_query.tar.bz2\'94 from https://www.pneumogen.net/gps/assigningGPSCs
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\f0\fs32 \cf2 Files required to run GPSC assignment using popPUNK:
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\f0\fs32 queries.txt: a list of paths to assemblies you wish to assign GPSCs to
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\f0\fs32 GPS_query: GPS reference database uncompress GPS_query.tar.bz2
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\f0\fs32 \cf2 output directory name is assigned using --output
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\f0\fs32 number of threads can be changed using --threads
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\f0\fs32 \cf2 Run GPSC assignment:
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\f0\fs32 poppunk --assign-query --ref-db GPS_query --distances GPS_query/GPS_query.dists --model-dir GPS_query --q-files queries.txt --output GPSC_assignment --threads 8 --no-stream --full-db --external-clustering GPS_query/gpsc_definitive.csv
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\f0\fs32 \cf2 Output files:
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\f0\fs32 _clusters.csv: popPUNK clusters with dataset specific nomenclature
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\f0\fs32 _external_clusters.csv: GPSC scheme designations
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\f0\fs32 \cf2 Novel Clusters: Will be assigned NA in the _external_clusters.csv as they have not been seen in the dataset used to designated the GPSCs. The popPUNK _clusters.csv file can be used to determine if NA isolates are the same cluster or not. Please email {\field{\*\fldinst{HYPERLINK "mailto:[email protected]"}}{\fldrslt \cf3 \ul \ulc3 \strokec3 [email protected]}} to have novel clusters added to the database and a GPSC cluster name assigned.
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\f0\fs32 Merged clusters: Unsampled diversity may represent variation between two clusters, GPSCs are the merged, for example if GPSC23 and GPSC362 merged the GPSC would be then reported to as GPSC23;362
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}