Closed AlessioMilanese closed 10 months ago
Ref-mOTUs are annotated using the NCBI annotation (from 8 January 2019) of the genomes within each ref-mOTU. This relates to mOTUs 2.5.1 and mOTUs 3.0.x.
Note that the ref-mOTUs annotation is derived directly from the specI annotation (which is done of 40 marker genes instead of the 10 marker genes used for mOTUs). From the specI annotation we additionally improve clusters where the majority of the genomes (at least 80%) agree into one annotation. For example a cluster composed of 100 genomes, where 99 genomes are annotated as Prevotella copri and 1 genome is annotated as Prevotella bivia, will be changed to be Prevotella copri. See also #72 and #76 for details.
Here is a summary of how the specI annotation was created:
Each specI is composed of 1 or more genomes. The annotation of speacIs is done progressively:
[From the next step we have an inconsistent NCBI annotations]
[From the next step we have weird annotations like "Candidatus Yanofskybacteria bacterium RIFCSPLOWO2_02_FULL_45_10" with almost no annotation at higher taxonomic level]
For the remaining weird annotation we try to solve them. There are two cases:
Hi, iv. There is no annotation because there were no genomes with valid names. It means "unassigned"?
Hi @Jibowe,
The one in (iv) are the ones that go to point 4.
They are still ref-mOTUs, they do not go to unassigned
. The unassigned
is explained here:
https://github.com/motu-tool/mOTUs/wiki/Explain-the-resulting-profile#unassigned
It is not clear how the annotation of the ref-mOTUs is created.