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


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?


nanopore assembly genome • 202 views
ADD COMMENTlink modified 6 weeks ago by trausch1.6k • written 6 weeks ago by rthapa40
gravatar for trausch
6 weeks ago by
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
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1561 users visited in the last hour