Compare repertoires

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After you have obtained a summary of repertoires, you can use compare.repertoires.py to compare 2 repertoires using similarity indices. We are using 3 different indices to compare the similarity of 2 repertoires

• Sørensen–Dice index

Given a directory with per sample immune repertoires

python ~/code/imrep/run.compare.repertoires.py $PWD/ ../imrep.pairwise.comparison/

The script will perform all pairwise comparisons. For each pairwise comparison, a directory will be created

Inside each such directory, you should expect the following files:

compare.similarity.CDR3.BrayCurtis.csv		
compare.similarity.CDR3.intersection.csv	
compare.similarity.VJ.Soerenson.csv
compare.similarity.CDR3.Jaccard.csv		
compare.similarity.VJ.BrayCurtis.csv		
compare.similarity.VJ.intersection.csv
compare.similarity.CDR3.Soerenson.csv		
compare.similarity.VJ.Jaccard.csv