We sometimes wish to exclude high-copy number, repetitive or otherwise difficult regions of the genome from polishing. This is easy enough to do with the --targets argument, but the resulting output includes only those places that were included in the targetlist. This leaves us with the task of piecing back together with a genome with the polished and non-polished sectoins.
Is it possible to return the entire input assembly when using --targets? If not, is this a feature you might consider implementing in future?
Hello,
We sometimes wish to exclude high-copy number, repetitive or otherwise difficult regions of the genome from polishing. This is easy enough to do with the --targets argument, but the resulting output includes only those places that were included in the targetlist. This leaves us with the task of piecing back together with a genome with the polished and non-polished sectoins.
Is it possible to return the entire input assembly when using --targets? If not, is this a feature you might consider implementing in future?