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!
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serene.s •
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
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.
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)
You may want to check the completeness first:
https://github.com/Ecogenomics/CheckM
This will assign taxonomy:
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!
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
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