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Structural variants detection from assembled genome from Nanopore sequence data

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

genome assembly nanopore
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updated by trausch trausch • written by rthapa • rthapa

1 answer

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

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written by trausch trausch

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

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written by rthapa • rthapa

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.

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written by trausch trausch

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

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written by rthapa • rthapa

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