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4.6 years ago
ben.blais
▴
10
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.
How similar are the sequences?
You can align them with
mummerand then parse the resulting alignment for variant positions with a custom script potentially.For FAST comparison, you could use
minimap2, see these example instructions https://github.com/lh3/minimap2/blob/master/misc/README.md#asmvarHello, 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 :)
When you say you couldn't get the differences, what do you mean exactly?
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?
See Mummer tutorial
https://mummer4.github.io/tutorial/tutorial.html
and the manual in the first paragraph of tutorial.
https://mummer4.github.io/manual/manual.html
There are a lot of helpful examples.
Mummer4 manual is below:
https://github.com/mummer4/mummer/blob/master/MANUAL.md