get repeats for bacteria and viruses to generate simulated reads of repeats

Question

[dabid]

I am trying to simulate reads of repeat regions of bacteria and viruses. I though a database of repeats for bacteria and viruses would be useful. I found RepBase which is a repeat database for Eukaryota, but not sure if I can find the same thing for prokaryotic (bacteria) and viruses.

Any hints?

[Gabriel R.]

Just a comment, we designed a read simulator for ancient genomics and metagenomics but it is still usable for modern metagenomics:
https://grenaud.github.io/gargammel/ In the package, there is a script to retrieve fasta genome files and build a composition vector of your sample: https://github.com/grenaud/gargammel/blob/master/src/microbial_fetcher/retrieveFromMetabit not the answer you are looking for but still, I thought it would help once you reach that stage :-)

Answer 1

[Jean-Karim Heriche]

MICdb may be what you're looking for (paper) but the website appears to be down.