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ParBLiSS / FastANI

Fast Whole-Genome Similarity (ANI) Estimation
Apache License 2.0
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[QUESTION] strain ANI #80

Closed alienzj closed 3 years ago

alienzj commented 3 years ago

Hi, FastANI team,

Can fastANI be used for distance calculation between strains? Especially for MAG, will an incomplete genome affect the strain's ANI calculation?

Thanks~ Jie

cjain7 commented 3 years ago

Yes it can. It really depends on how "incomplete" the genome is. In the FastANI publication, we show its applicability to MAGs.

alienzj commented 3 years ago

Hi, thanks for your reply.

Most metagenome-assembly-genome is incomplete, although a MAG has 99% completeness assigned by CheckM, especially judging from the number of contigs, there are still many gaps in the entire genome.

So I am very worried about whether clustering can be done at the strain level based on the value of ANI.