I am aligning multiple bacterial genomes and I would like to know how I can obtained a % of identity between these genomes ?
Is that a function that can be displayed by either Mugsy or Mauve?
Thank you for your answers.
I recommend Mash
mash dist genome1.fna genome2.fna
Thank you for your help.
I used mash and I have the following results :
Mygenome.fasta Close_genome_1.fasta 0.0196 0494/1000
Mygenome.fasta Close_genome_2.fasta 0.0174 530/1000
I do not really understand the meaning of the two scores.
In this case, which genome is closer? Genome 1 or 2?
Thanks in advance
Close_genome_2 is closer. ANI = 1 - mash distance, so here 1 - 0.0174 = 0.9826, i.e. 98.26% similarity. The last column displays the number of shared hashes (out of 1,000 by default). You can get more precise results if you sketch your genomes first with e.g. k-mer value of 17 and sketch size of 10,000 (mash sketch -k 17 -s 10000 input.fna) and then compare the resulting .msh files with mash dist
ANI = 1 - mash distance
1 - 0.0174 = 0.9826
mash sketch -k 17 -s 10000 input.fna
What you're probably looking for is average nucleotide identity (ANI).
This is a tool I ever wanted to test, but now it's not relevant for me anymore
More readings from my simple web search
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