repeat_database for complex metagenomics data?

[mmpust]

Hi, can I use Transposome for annotating transposable elements from paired-end metagenomics data of complex microbial communities? If so, what would be the repeat_database in the config file?
Thanks!

[sestaton]

Hi @mmpust,

This is an interesting question! In theory this could work but you would need a representative database from the taxa under investigation which could be generated de novo with a k-mer based approach or RepeatScout. I have to admit I am not an expert on metagenomics and without knowing the type of sample or what taxa you would expect it is hard to provide specific guidance.

If you can provide more information I may be able to help on the database question but I will also do some research and get back to this question next week.