Best way to compare genome files similarity

Question

[Platelet Guardian]

Hi,

I am new to bioinformatics and would like to know if there is any recommended software to compare for example:

Let's say I have multiple files (fasta for example) from complete genomes and want to compare their similarity % or/and if they share the same origin.

Something like different bat coronavirus and human genomes.

I tried to make my own python script but it is a hassle and very time consuming.

Thanks

[Platelet Guardian]

Is there any way to do this using R?

Answer 1

[Mensur Dlakic]

FastANI rapidly compares fasta sequences and will output global identity. It is meant only for relatively similar genomes, and will not create any output if identity is below 75-80%.

[Platelet Guardian]

This sounds useful as I used pairwise using blastn and achieved 96% and 85% per ident for the sequences that were supposed to be similar when compared to the main sequence. The other sequences had bad e-values and similarity lower than 67%.

Answer 2

[shenwei356]

Sourmash can compare multiple genomes/reads using FracMinHash and build a tree.

Answer 3

[Istvan Albert]

MAFFT is another tool that could also employ

https://mafft.cbrc.jp/alignment/software/

that being said the task of comparing bat coronaviruses is incomparably simpler than comparing human genomes.

radically different methodologies would be needed in the latter case.