Question: Find repeat regions on 100 eukaryotic assemblies
gravatar for Chvatil
10 weeks ago by
Chvatil60 wrote:

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.

repeat assembly • 104 views
ADD COMMENTlink modified 10 weeks ago by colindaven2.6k • written 10 weeks ago by Chvatil60
gravatar for colindaven
10 weeks ago by
Hannover Medical School
colindaven2.6k wrote:

You can have a look at MAKER for annotation.

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

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

ADD COMMENTlink written 10 weeks ago by colindaven2.6k
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