This program filters tandem repeats generated by the Tandem Repeat Finder [1] for those suitable as a label with CRISPR-dCas9 [2].

First, generate the appropriate .dat file with the TRF, for example:

trf some_sequence.fa  2 7 7 80 10 80 1000 -d

Then, run the trf_filter.py script in this repository on the output:

./trf_filter.py some_sequence.dat --index mm10 --matches=20 --length=20 --pam "NGG" 

where the --index value is a bowtie2 index you have created. For help on the options, run ./trf_filter.py --help.