Dereplicate MAGs on strain level

[alienzj]

Hi, wwood,

Recently, my colleagues and I are using galah to construct MAG cluster. Most studies only do clustering at the species level. Can galah be used at the strain level? You know, we are not only concerned about the genomes of the selected representatives, but also about the members of each cluster.

Thanks.
Jie

[wwood]

Hi,

I'm afraid not really. Higher than 99%, FastANI doesn't give overly useful results, in my rather short experience of trying that. At that level you might be better off making strain trees.

[alienzj]

Hi, thank your guide.

My colleagues and I want to make a complete genome from a strain cluster of MAGs. So the more accurate the strain clusters, the less contamination, and the generation of chimeras should be avoided as much as possible.
We have tried to make a consensus genome on some species cluster, although the completeness is improved, it also produces a high contamination rate and strain heterogeneity rate. Maybe something went wrong in our approach from the beginning.

Anyway, thanks again.
I like rust, I like galah.