I've assembled 14 scaffolds of a chloroplast genome and would like to join them into a single scaffold according to a closely-related reference. ABACAS seems to be the only tool for that, so I tried it. With default parameters, the output scaffold had a lower reference coverage (92%) than the original scaffolds (99%). Do you know why that happened? My original scaffolds were all longer than 500bp, so ABACAS could not have filtered those out. If you've worked with ABACAS before, could you give some tips/advice on getting good results?
The reference coverage was found with QUAST.