CoreDetector for large repeat unmasked genome?

[bijendrabio]

Hello,
Curious if you have tested CoreDetector using repeat unmasked version of large plant genomes?

Kind regards,
B

[RussellAndrewEdson]

Hi B, sorry for the late reply!

Mario reckons that for genome sizes up to 3GB they tested unmasked and that worked well. For a wheat genome, only repeat-masked has been tested (and in that case, he recommends splitting up the wheat genome into 3GB chunks--e.g., 1A, 1B and 1D to one chunk, and so on--and that should work well). At the end you can concatenate the results of chunks into one single MAF file.