[maker-devel] Using PacBio and Illumina in MAKER

[Timo Metz]

Hey guys,

I was wondering on what would be the best way to implement Pacbio long and
assembled Illumina short reads into MAKER. PacBio reads have a higher
confidence to find correct gene models as they do not need to be assembled,
but I do not have enough PacBio reads available to construct an annotation
solely based on PacBio reads. I also have tons of short reads available,
but those are really short (30-40bp) so they are not very reliable. Is it a
good idea to first do an annotation only with PacBio reads and Protein data
and then do a "re-annotation" with Illumina reads in order to only identify
"new" models that could be introduced by Illumina reads but let the old
models intact? Are there any other suggestions or experiences?

best
Timo
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