assign taxonomy to bins

Question

[serene.s]

Hi Guys! I did the assembly of one of my metagenomic samples using the megahit tool and then binned the resultant contig.fa file using MaxBin2 software but now I want to assign taxonomy to the bins. How can I do that? I want to assign taxonomy till the species level if possible for the bins whose completeness is more than 90%

Thanks!

Answer 1

[andres.firrincieli]

You can use GTDB-Tk but you will need at least 150 GB of RAM. In case you do not have access to a cluster, you can use GTDBTk from KBase

[Mensur Dlakic]

More like 220 Gb of RAM with the latest version.

EDIT: I meant the 2021 version. It seems like a new version came out 10 days ago, and I have no idea about its RAM requirements.

[andres.firrincieli]

I didn't use gtdb-tk in a while but the latest version (v2.0.0) has lowered the RAM requirements, to approximately 35 GB, by splitting the reference tree into multiple subtrees.

edit: version v2.0.0 has a bug which force the user to use the full tree approach (--full-tree flag) (link)

Answer 2

[Mensur Dlakic]

You may want to check the completeness first:

https://github.com/Ecogenomics/CheckM

This will assign taxonomy:

https://github.com/Ecogenomics/GTDBTk

Answer 3

[serene.s]

Hi Thanks for your responses. I am not sure about the RAM of 320 GB of our server I looked into KBase but I am not able to understand if I have to separately install the GTDB tool from their website or I can upload the bin files on KBase's server and submit the job for taxonomic assignment?

Thanks!

[andres.firrincieli]

GTDB is already installed in KBase. You just need to upload the bin files and run the job.

here is a short tutorial on how to upload the data on kbase and run specific jobs: link