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Russel88 / CRISPRCasTyper

CCTyper: Automatic detection and subtyping of CRISPR-Cas operons
https://typer.crispr.dk
MIT License
89 stars 16 forks source link

add repeated sequence to repeats.fa #25

Closed fabgenomics closed 2 years ago

fabgenomics commented 2 years ago

Hi, I wanted to use your program to get E. coli spacers. It work well on some of my strains but for some of them there are missing spacers due to some mismatch in the last repeat sequence. Is there a way to update the repeats.fa file in the db folder with my own list of repeated sequences ? Have a nice day, Fabien

Russel88 commented 2 years ago

Hi Fabien,

Yes you can. If you use conda you can find the db directory inside the conda environment. Then you simply add your repeats to the repeats.fa file (give them unique names, not overlapping with any of the other names). When you run cctyper with the conda environment it will then use the updated file.

However, the repeats.fa is only used if minced is not finding a CRISPR array near a cas operon. Therefore, it will most likely not make any difference for you