Alignment of assembly on reference genome with MiniMap2 returns false unmapped contig

Question

[gallinaro.martina]

Hi everybody, I have used MiniMap2 to map an assembled genome (generated with oxford nanopore reads) on a public reference, I did it to find the regions in common and not in commond between these two because I want to do a pangenome by adding to the reference the part of the assembly not present in the reference. I used the originated bam file to find the uncovered part by using samtools depth and taking only regions with depth=0 but when I blast these regions on my reference I had an hit.

Could somebody suggest me how is it best to align an assembly on a reference genome to take what is not present in my reference genome?

this is the command I used to align:

minimap2 -a -x asm20 ref.fa query.fa

thank you all

[5heikki]

How about splitting your assembly into short overlapping reads and mapping them on the reference with e.g. bowtie?

[GenoMax]

Could somebody suggest me how is it best to align an assembly on a reference genome to take what is not present in my reference genome?

Not sure what you mean by "to take what is not present" but if you are aligning large assemblies to a reference then you should give mummer4, mauve or lastz a try.