Low quality genomes end up as seperate species.

[SilasK]

Low-quality genomes cluster apart. I used galah on large datasets. What I noticed is that often a low complete genomes are selected as separate species, which are then annotated by GTDB-tk as the same species as other high-quality genomes.

I have the impression that if a genome has low completeness it will not pass the min coverage of FastANI and so yield no FatANI report. I don't know how you do this internally but I imagine they perturb the clustering.

Would the solution simply be to use a very low --min-aligned-fraction?

[Gsmith535]

This may be too little too late.

Consider this hypothetical scenario: a genome is split exactly in half into two bins. GTDB-tk will discover that both are the same species because the marker genes encoded match the same member of the database. However, they are simply not directly comparable with something like ANI (or even AAI) because there are (virtually, ignoring duplications and other possibilities) no shared regions in which any amount window of bps in one bin are similar to another. Reducing the minimum % identity, aligned fraction, fragment length, etc. will not help to compare and pick a representative despite being the same species.

I believe this is part of the rationale behind minimum completeness and maximum contamination parameters in dereplication programs.