I have 10 paired end samples. I have done the quality check and trimming then I merged the trimmed reads and after that I have done the mapping using minimap2 using this command:
minimap2 -ax map-ont ref.fna(reference genome) trimmed.fq(merged trimmed reads) >aln.sam
I want to do the assembly now, but I don't find any tool where I can use this sam file
Please help me with this.