Question: Structural variants detection from assembled genome from Nanopore sequence data
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gravatar for rthapa
6 weeks ago by
rthapa40
rthapa40 wrote:

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

nanopore assembly genome • 202 views
ADD COMMENTlink modified 6 weeks ago by trausch1.6k • written 6 weeks ago by rthapa40
0
gravatar for trausch
6 weeks ago by
trausch1.6k
Germany
trausch1.6k wrote:

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

ADD COMMENTlink written 6 weeks ago by trausch1.6k

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

ADD REPLYlink written 6 weeks ago by rthapa40

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.

ADD REPLYlink written 6 weeks ago by trausch1.6k

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

ADD REPLYlink written 5 weeks ago by rthapa40
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