Taxonomic classification of MAGs

Question

[c.e.chong]

Hi all,

I am looking for some advice regarding taxonomic classification of MAGs from skin Metagenomics samples.

I have binned my contigs using CONCOCT via Anvio which gives me completeness, redundancy and taxon information for each bin. I then dereplicated the genome bins and now have representative genomes from different skin states. The genomes include both fungal and bacterial genomes. I have taxon information for the dereplicated genomes as I know what bin they came from and the taxon of that bin, but is there another way to get strain resolution for my MAGs? I need any databases etc to contain fungal info as well as prokaryotic and achaean info.

Thanks in advance!

Answer 1

[Mensur Dlakic]

For prokaryotes, this database should be useful:

https://gtdb.ecogenomic.org/

You can make your own classification using their toolkit:

https://github.com/Ecogenomics/GtdbTk