Assembly based structural variants call from bacterial genome

Question

[rthapa]

Hi,

I am trying to call structural variants from assembled bacterial genome. The genome is assembled using Nanopore long reads and is polished with Illumina reads using Pilon. The coverage of nanopore reads is ~80X. I wonder if assembly based structural variants call would be better than mapping based approaches. Does anyone have suggestion based on their experiences?

Thanks

[samuel.a.odonnell]

Assuming your assembly is correct and complete then whole genome alignment methods will be more accurate than read mapping methods. I have tried both on S. cerevisiae genomes and found this.

You can try my tool MUM&Co or Syri for a full range of SV types.

[rthapa]

Thank you. Is it possible to call SV by comparing multiple genomes with reference genome using MUM&Co? The script can take only single query genome at a time.

bash mumandco.sh -r ./yeast.tidy.fa -q ./yeast_tidy_DEL100.fa -g 12500000 -o DEL100_test

[samuel.a.odonnell]

I've replied on the github. If you are looking to generate a multiple whole genome alignment and call SVs then you may want to look at the vg toolkit for genome graph variant calling