Structural variants detection from assembled genome from Nanopore sequence data

Question

[rthapa]

Hi,

I have assembled and polished the genome from long read sequences with canu and pilon respectively. I wonder if it is possible to call structural variation by comparing the contig with the reference sequence. I see that there are many tools available to detect SV using the raw reads. Does anyone have suggestions if using polished contig is possible to detect SV?

Thanks

Answer 1

[trausch]

There are multiple options, mingraph for instance has SV calling or pav.

[rthapa]

Thanks a lot. I will try minigraph. Just a question, is it preferred to use raw fastq reads for calling variants than assembled genome?

[trausch]

That's a matter of the assembly quality. If you have low coverage data you may also want to try mapping-based SV discovery approaches such as Sniffles or delly for long-reads.

[rthapa]

I tried using minigraph for SV calling by comparing one assembly to reference genome. It gave me the bed file of SV. When I tried using multiple samples, the gfa file is empty. Do you have any idea? Thanks