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nextgenusfs / funannotate

Eukaryotic Genome Annotation Pipeline
http://funannotate.readthedocs.io
BSD 2-Clause "Simplified" License
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TanTan with a repeatModeler consensus library #986

Closed Malabady closed 4 months ago

Malabady commented 7 months ago

Hello,

Is the default masking method "Tantan" suitable when giving a RepeatModeler-created repeat library?

Thanks, Magdy

UmerFarooq17 commented 6 months ago

I asked someone about the use of "TanTan" to mask genomes, but the suggested not to use it. So i used RepeatModeler to create repeat library then used RepeatMasker. then is used that repeatmasked genome.fa file for annotation with funannotate skipping the "FUNannotate Mask" step.

Malabady commented 6 months ago

That's what I ended up doing. Thanks, Umer.

hyphaltip commented 4 months ago

tantan is fast and does not have licensing restrictions for folks in industry but repeatmodeler + repeatmasker (or EDTA + repeatmasker) are going to be more sensitive tools for finding diverse TE families to mask.