Maybe can be merge with the DeNovoRepeatLib pipeline (see #32).
The purpose of RepeatMaskMyGenome is to repeat mask a genome based on a repeat library (made de novo or provided within a lib e.g dfam or RepBase).
Having this pipeline could help to move easily to other annotation tool than MAKER if needed.
This pipeline consist in mains 3 steps:
split the genome into chunks (overlap or not? we can see in MAKER code to see how they do.)
Mask the chunks
Merge the annotation of the different chunks (if overlapping chunks we need to find a way to resolve the merge in a good way)
Input:
Path to a lib (fasta file is de-novo a name if from DFam or RepBase)
See #17 for the general picture.
Maybe can be merge with the DeNovoRepeatLib pipeline (see #32).
The purpose of RepeatMaskMyGenome is to repeat mask a genome based on a repeat library (made de novo or provided within a lib e.g dfam or RepBase). Having this pipeline could help to move easily to other annotation tool than MAKER if needed.
This pipeline consist in mains 3 steps:
Input:
Output: single gff file + stats