How to get list of different bases and their positions from an alignment?

Question

[SaltedPork]

I am aligning two viral genomes which I am expecting to be >90% similar. I would like a list of the changes (from one base to another) and their locations in the genome. Which program(s) can I use to achieve this? I have already tried lastz's --census option, but it only tells you if a base is aligned, not whether it is identical. Thanks.

[WouterDeCoster]

Hi SaltedPork,

I have reopened this question, there is not really a need to delete it.

Cheers,
Wouter

[finswimmer]

Hello,

is your data from a sequencing project or do you just have the reference sequences you like to compare?

fin swimmer

[SaltedPork]

Hi, just the sequences i'm comparing.

[finswimmer]

Hi,

how have you done the alignment? How does the output look like?

fin swimmer

[SaltedPork]

they are about 92% similar, ~700 base difference

[GenoMax]

That does not answer @finswimmer's question about format of the output.

Answer 1

[WouterDeCoster]

If I understand correctly you want to align to reference genomes and find the differences. If so, you could try minimap2 to align both using the -cx asm5 option. Scripts are available in that repo (paftools) to get the differences.