I have corrected PACBIO assembly of a plant genome (query) and would like to polish the assembly with ONT reads and Illumina (target.fastq). I am using Minimap2 but it gave me .sam and .paf output like below.
minimap2 -ax map-ont ref.fa ont-reads.fq > aln.sam (I am not sure where the polishing has been done. How can see if the gaps has been filled?)
minimap2 -a ref.fa ont-reads.fq > aln.paf (This give me target coordinates that I want to extract the sequence for to see if there is any overlapping between PACBIO/ONT/ILLUMINA.
Any suggestion is welcome?