BVAB1 species level assignment

[kviljoen]

Hi there,

I'm wondering about the assignment of BVAB(1/2/3) as you say that VALENCIA only considers species level annotation for Lactobacillus, Gardnerella, Prevotella, Atopobium and Sneathia, but you also say that "CST IV-A contains a high to moderate relative abundance of BVAB1 and G. vaginalis" and "CST IV-C contains low relative abundances of G. vaginalis, BVAB1, and Lactobacillus spp. and includes". Please can you clarify?

Regards,
Katie.

[michaelfrance]

Hi Katie,

Apologies BVAB1 is a species level assignment, it just didn't occur to me because it's name hasn't been finalized. If you look at the column headings of the reference centroids file, you can see exactly what is expected.

Hope this helps,

Michael

[kviljoen]

Thanks for the prompt response Michael.

I see you have BVAB1, BVAB2.BVAB3, BVAB_TM7 and Shuttleworthia_satelles which would require manual curation in external datasets such as ours. Do you have reference seqs or accession numbers listed somewhere that you used for these?

Thanks again,
Katie.

[kviljoen]

Hi Michael,

We do have BVAB1 annotated in our dataset under the Species column, but the convert_qiime.py script doesn't appear to be setup to pick up any BVABs. The resulting merge file does not contain BVAB, which affects the CST assignments by Valencia.py?

Regards,
Katie.

[Gscorreia89]

Hi,

I have a somewhat similar situation: more specifically, I am trying to run VALENCIA with taxonomic assignments generated by SILVA. I am also keen to find out which sequences were used to assign BVAB's and Shuttleworthia. Are these sequences from STIRRUPS DB?

Best Wishes,
Goncalo

[luhugerth]

In the same vein - it's impossible from the data here to know which species belong to e.g. "Ruminoccocus_2" vs "Ruminoccocus_3". Just letting us know the exact procedure used for annotating the samples used for the centroids would help with a lot of troubleshooting...