Comments (2)
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.
from galah.
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.
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Related Issues (20)
- Update fastANI requirement to 1.31 HOT 1
- Galah not clustering MAGs with ANI greater than the threshold HOT 3
- --min-aligned-fraction, as fraction?
- sketches in pre-cluster for a little bit distant related genomes HOT 4
- dashing2 instead of dashing1
- Regarding galah output HOT 6
- If input genomes are short, they don't cluster
- Dashing failed HOT 1
- Intermediate output
- Low quality genomes end up as seperate species.
- Wrong genome annotation
- Compilation error HOT 2
- add bindash support instead of dashing HOT 1
- checkM table not working HOT 1
- Failed to find sufficient version of dashing HOT 1
- unnecessary fastani check
- Finch running time HOT 1
- skani is not parallelized in `galah cluster` HOT 2
- error: unexpected argument '-d' found HOT 2
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