I previously assembled a fungal genome with Illumina Hi-Seq paired-end sequences. The assembly was ~ 32Mbp and was made up of ~ 400 contigs. I did not try to join the contigs into scaffolds. BUSCO determined that the assembly was ~98% complete based on the number of orthologs.
However, I just received PacBio sequences from the same isolates and want to use them improve the assembly and possibly close the genome. My question is asking if I should reassemble the Illumina reads and PacBio reads together using SPAdes or some other hybrid assembler, or if I should update the pre-existing Illumina assembly with PacBio using PBJelly?
Thanks in advance! Morgan