One issue we've noted is the presence of short sequence fragments for some microhap sequencing runs, presumably from the formation of primer dimer. For now, we're merging with Flash and then discarding short merged sequences prior to running mhpl8r pipe. We could easily incorporate such a step into the automated end-to-end workflow for both paired-end (post merging) and single-end data.
One issue we've noted is the presence of short sequence fragments for some microhap sequencing runs, presumably from the formation of primer dimer. For now, we're merging with Flash and then discarding short merged sequences prior to running
mhpl8r pipe. We could easily incorporate such a step into the automated end-to-end workflow for both paired-end (post merging) and single-end data.