Repeat detection/masking in bacteria

Question

[liorglic]

Hi there,

In eukaryote genome annotation, repeat masking is an important step in a genome annotation pipeline, and there are many dedicated tools and pipelines (RepeatMasker, RepeatModeller, EDTA, etc.).

I was asked to help with repeat detection in bacterial genomes, but as far as I can tell, this is not a very common thing to do. For example, the popular annotation Prokka doesn't seem to have a repeat masking step. Am I correct?

Can someone with experience working with bacterial genomes suggest some tools or methods for repeat detection and annotation? I am looking for a tool that will get a genome assembly and return some form of repeat annotation.

Thanks!

Answer 1

[Brian Bushnell]

In BBTools, bbmask.sh can mask STRs (with repeat length 1-15bp), and findrepeats.sh can find and report or mask longer and partial repeats of various types. However, there's no reason to mask them on bacterial genomes prior to annotation.

Answer 2

[Mensur Dlakic]

Minced identifies CRISPR repeats:

https://github.com/ctSkennerton/minced

[liorglic]

Thanks. How about other types of repeats?

Answer 3

[Max Sikolenko]

RepeatFinder detects repeats in DNA sequences: https://github.com/deprekate/RepeatFinder/.

It doesn’t perform any annotation, though. It just finds repeats and reports their coordinates.