[maker-devel] processing of simple and complex repeats

[Santiago Revale]

Dear Maker developers,

Can Maker distinguish between simple and complex repeats from a gff3 file of pre-aligned repeats?

I'm trying to annotate a genome of a non-model Drosophila species and I've already generated a gff3 file with both simple and complex repeats for this species. I would like to use this gff3 file as input for Repeat Masking so Maker won't have to align repeats from any library. My maker_opts.ctl file looks like this:

#-----Repeat Masking
model_org=
rmlib=
repeat_/path/to/te_proteins.fasta
rm_gff=/path/to/Dato_genome.Dato-first.full_mask.out.reformat.gff3
prok_rm=0
softmask=1

By using softmask=1 I understand that Maker will softmask only low complexity repeats (while complex ones will be hardmasked). My question is whether Maker can distinguish between simple and complex repeats from the gff3 file in order to softmask only simple repeats. Also, do you think it would be better to only include complex repeats in the gff3 file and let Maker find simple repeats on its own by using model_org=simple?

Thank you very much in advance.

Best regards,
Santiago

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