Genome Taxonomy Database (GTDB)
GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes.
See the GTDBTk homepage for more info.
First, we need to download the GTDB database files. The database is pretty big (64 Gb), so even downloading it from our local copy in the de.NBI Cloud will take a couple of minutes. After downloading, we need to extract the tar archive (please be patient ;):
cd /mnt
wget -qO- https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/denbi-mg-course/gtdbtk_v2_data.tar.gz | tar xvz
Now we need to set an environment variable that stores the path to the database and put GTDBtk in our path:
export GTDBTK_DATA_PATH=/mnt/release207_v2
We need to download the mash database, since it takes some time to create:
cd /mnt/release207_v2
wget https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/mg_databases/mash.msh
Next, let’s assign taxonomic labels to our binning results using GTDB-TK:
cd /mnt/WGS-data/megahit_out/maxbin
gtdbtk classify_wf --extension fasta --cpus 28 --genome_dir . --out_dir gtdbtk_out --mash_db /mnt/release207_v2/mash.msh
When you are done, also compute the classification for the metabat binning, since we will need the results for the submission:
cd /mnt/WGS-data/megahit_out/metabat/final.contigs.fa.metabat-bins...YOUR_FOLDERNAME
gtdbtk classify_wf --extension fa --cpus 28 --genome_dir . --out_dir gtdbtk_out --mash_db /mnt/release207_v2/mash.msh
However, the classification was quite fast due to mash/ANI fast identification (see https://ecogenomics.github.io/GTDBTk/commands/classify_wf.html). Marker gene based classification did not happen, we will repeat the classification with another - non artifical - sample. Create a new folder and download the data:
mkdir /mnt/mgexample/
cd /mnt/mgexample/
wget https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/mgexample/examplesample.tar.gz
tar -xzvf examplesample.tar.gz
We will do the process for the maxbin results again, step by step:
gtdbtk classify_wf --extension fasta --cpus 28 --genome_dir examplesample --out_dir gtdbtk_out --mash_db /mnt/release207_v2/mash.msh
Load gtdbtk.backbone.bac120.classify.tree, gtdbtk.bac120.classify.tree.3.tree into the ncbi taxonomy viewer:
https://www.ncbi.nlm.nih.gov/tools/treeviewer/
Convert to itol format:
gtdbtk convert_to_itol --input_tree gtdbtk_out/classify/gtdbtk.backbone.bac120.classify.tree --output_tree test.itol
Load into: