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Compare two sequences and obtain differences

Hello everyone, I would like to know if it is possible to align two sequences of 38 000 000 bases between them and to obtain a file corresponding to the differences between these two strains. I can visually see these results with IGV but I can not get the differences. Thank you and wish you a great day.

assembly genome alignment
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written by ben.blais • ben.blais

How similar are the sequences?

You can align them with mummer and then parse the resulting alignment for variant positions with a custom script potentially.

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written by Joe Joe

Hello, thanks for your answers. I wanted to use MUMmer, but I can not get the differences between the sequences. One of the sequences is my reference, the other is a sequence obtained after assembly (Sequence b). I would like to be able to align the sequence B on the reference sequence in order to recover the differences (variants). I try to use Minimap2 too. Thanks you :)

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written by ben.blais • ben.blais

When you say you couldn't get the differences, what do you mean exactly?

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written by Joe Joe

Hi and thanks you :) , when I use MUMmer I get a delta file but I do not know what to do with it. I would like to get the list of the differences between the sequence and the reference as a variant call (Position, base reference, alternative base). Is it possible with MUMmer?

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written by ben.blais • ben.blais

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