Mauve alignment vs samtools for SNP calling

Question

[gabriel.jabud]

If I have two assembled genomes (one reference), what is the difference between doing SNP calling using something like Samtools from the raw Illumina reads and doing a Mauve alignment after assembly of each genome? Would Samtools be much more accurate? It seems easier to just do a Mauve alignment and extract the SNPs since I've already done the assemblies but maybe this is oversimplifying it. These are bacterial genomes if that matters.

Answer 1

[Joe]

You should use the reads and samtools if you have them. Part of identifying SNPs etc is determining how well they're supported (i.e. are they real or sequencing errors for instance). If you aligned 2 genomes with mauve, firstly it will be horribly inaccurate as you say, but also you'll have no information about whether that SNP is supported in most or all of the reads covering that position.

[rthapa]

Is it better to use assembled genome if the assembly is completed using nanopore reads (~100x coverage) and polished using short reads for calling SNPs and structural variants?

[Joe]

Better than what alternative?

[rthapa]

Better than using map based based tool?

[Joe]

I'm not really sure what you are asking, but yes, a nanopore assembly polished with short reads is the best to have SNPs called against.

You can map the short reads back against the hybrid assembly to get your SNPs and SVs.

[rthapa]

Thank you. I am planning to compare the hybrid assembly to reference genome to call the SNPs and SV.