I'm diving into the world of long read sequencing. I want to do some quality filtering of my reads using Filtlong. According to the author filtering using a reference is a better way to go in comparison to quality parameter based filtering. I understand the reasoning behind it but my question is the following:
If I pick a reference from RefSeq and use the short reads as a filtering guide, does that mean that anything not present in this ref will be filtered out (plasmids for example)?