Visualizing whole genome alignment beyond dotplots

Question

[Lina F]

Hi all,

I de novo assembled two microbial strains of the same species into four contigs each. I assume they will be very similar in sequence, but I would like to know if there are SNPs or Indels.

I tried both mummer and Last to align the two genomes and I was able to generate dot plots, but they are mostly useful to give me an overview of the alignment.

I tried loading the maf file that Last produced into Geneious, but that did not work. Converting the MAF file to VCF (which Geneious would be able to open) also doesn't seem trivial.

Can you recommend a tool that lets me visualize differences on a SNP/Indel level?

Any suggestions are appreciated!

Cheers,

~Lina

Answer 1

[h.mon]

For visualizing microbial whole genome alignments, Mauve is really nice. If I remember correctly, you can even see the DNA alignment - but scrolling wasn't good.

However, for the purpose of finding SNPs and indels in two closely related strains, I would use one assembly as reference, and map the reads of the other strain (or both) into this reference and call the variants. This way you can apply quality filtering steps which will decrease the number of false positives. In this case, you can look at SNPs and indels vcf file using IGV.

[Lina F]

I have tried Mauve and I agree, the scrolling is not great.

What kind of mapper would you recommend for calling SNPs, given that I have long contigs, not short Illumina reads?

[h.mon]

Did you use long reads (PacBio or Nanopore) to assemble?

[Lina F]

Yes, I have two de novo assemblies from long read data.

I actually also have Illumina data (I used it to error-correct the assemblies) but my main question here is what kind of differences exist between the two assemblies.