Find repeat regions on 100 eukaryotic assemblies

Question

[Chvatil]

Hello everyone, I have a hundred genomes and I'm looking for repeated regions along these assemblies.

First of all, I thought of using RepeatModeler, only the most familiar among you know that it is not at all optimized software that requires a lot of resources and calculation time, which is therefore not feasible in my case.

So I would have liked to know if any of you had an alternative solution that was faster and more feasible on a large number of insect genomes?

I thought for example to use a blastn approach by using in query the assemblages and in database of nucleotide databases containing ETs, which would be an approach maybe less sensitive but much faster! Only I can't find a database in ET representative of eukaryotes (Repbase is not free).

Thanks a lot.

Answer 1

[colindaven]

You can have a look at MAKER for annotation. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-491

The DFAM database might help for data, but I don't know if that covers your insects.

https://dfam.org/

Perhaps for large scale projects like this you need to apply for compute time on an available cluster.