Examples

The very basic way to run ImReP is to use the following command:

$ python imrep.py reads.fastq clonotypes.txt

In case if the user is targeted at assembling CDR3 regions from IGH chain, it should be specified like this:

$ python imrep.py -c IGH reads.fastq clonotypes.txt

Running ImReP for mouse:

$ python imrep.py -c IGH -s mouse reads.fastq clonotypes.txt