I am looking for a software that can identify long sequences (1500-2000 bp) that occur more than once in my genome of interest. A k-mer counter like KMC could have worked, but KMC has a max limit of 256 bp. If I can club contiguous 256-mers from KMC, that would work too, but I don't know how to do that. Any ideas?
MUMmer includes a
repeat-match tool which can do exactly that:
$ repeat-match USAGE: repeat-match [options] <genome-file> Find all maximal exact matches in <genome-file> Options: -E Use exhaustive (slow) search to find matches -f Forward strand only, don't use reverse complement -n # Set minimum exact match length to # -t Only output tandem repeats -V # Set level of verbose (debugging) printing to #
Note that a "maximal exact match" is just a maximal repeat.
1$\begingroup$ This looks ideal. Will try this out and update. Thank you! $\endgroup$– PSiddyMay 4, 2021 at 15:31
1$\begingroup$ Okay I tried it out and it worked, so thank you! Ended up using mummer instead of repeat-match so as to compare between (and not within) sequences $\endgroup$– PSiddyMay 5, 2021 at 22:24