Optional repeat library construction and genome repeat masking

andreaminio / AnnotationPipeline-EVM_based-DClab

Cantù Lab @ UC Davis - Annotation pipeline - EVM based

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Optional repeat library construction and genome repeat masking #8

Open yaoxkkkkk opened 6 months ago

yaoxkkkkk commented 6 months ago

I noticed that this section seems to be lost: (optional) Custom repeat library construction, it returned to the home dir of these files.

And it seemed that the pipeline didn't mention genome repeat mask, I am curious about that, because all instructions I have ever seen tell me repeat mask is necessary.

yaoxkkkkk commented 6 months ago

Just a remind: the pipeline requires BUSCO v3, now BUSCO has updated to v5, so the default gene predictor has changed to Metaeuz instead of Augustus. The output would be slightly different with the pipeline. Just switch gene predictor of busco v5 to augustus and everything would be fine.