gtdb_to_taxdump

Convert GTDB taxonomy to NCBI taxdump format.

NOTE: the taxIDs are NOT stable between releases! See gtdb-taxdump for an alternative that uses stable taxIDs.

Table of Contents

• gtdb_to_taxdump
• Summary
  • WARNING
  • Citation
• Install
  • From pypi
  • From github
• Usage
• Extras
• GTDB website

Summary

Convert GTDB taxonomy to NCBI taxdump format in order to use the GTDB taxonomy with software that requires a taxonomy in the taxdump format (eg., kraken2 or TaxonKit).

Note that the taxIDs are arbitrarily assigned and don’t match anything in the NCBI! Running gtdb_to_taxdump on a different list of taxonomies (e.g., a different GTDB release) will create different taxIDs. See GTDB-taxdump for a method to produce stable taxIDs (recommended!).

WARNING

There was a serious bug with ncbi-gtdb_map.py prior to version 0.1.5. Many of the taxonomic classifications are likely incorrect. Please re-run the analysis. I’m sorry for any inconvenience.

Citation

Install

Dependencies

• numpy
• networkx
• taxonkit

Package

From pypi

pip install gtdb_to_taxdump

From github

pip install git+https://github.com/nick-youngblut/gtdb_to_taxdump.git

Usage

See gtdb_to_taxdump.py -h

Example (GTDB release202):

gtdb_to_taxdump.py \
  https://data.gtdb.ecogenomic.org/releases/release202/202.0/ar122_taxonomy_r202.tsv.gz \
  https://data.gtdb.ecogenomic.org/releases/release202/202.0/bac120_taxonomy_r202.tsv.gz \
  > taxID_info.tsv

Example (GTDB release95):

gtdb_to_taxdump.py \
  https://data.gtdb.ecogenomic.org/releases/release95/95.0/ar122_taxonomy_r95.tsv.gz \
  https://data.gtdb.ecogenomic.org/releases/release95/95.0/bac120_taxonomy_r95.tsv.gz \
  > taxID_info.tsv

Example (GTDB release89):

gtdb_to_taxdump.py \
  https://data.ace.uq.edu.au/public/gtdb/data/releases/release89/89.0/ar122_taxonomy_r89.tsv \
  https://data.ace.uq.edu.au/public/gtdb/data/releases/release89/89.0/bac120_taxonomy_r89.tsv \
  > taxID_info.tsv

You can add the taxIDs to a GTDB metadata table via the --table param. For example:

wget https://data.ace.uq.edu.au/public/gtdb/data/releases/release89/89.0/ar122_metadata_r89.tsv
gtdb_to_taxdump.py \
  --table ar122_metadata_r89.tsv \
  https://data.ace.uq.edu.au/public/gtdb/data/releases/release89/89.0/ar122_taxonomy_r89.tsv \
  https://data.ace.uq.edu.au/public/gtdb/data/releases/release89/89.0/bac120_taxonomy_r89.tsv \
  > taxID_info.tsv

Extras

• ncbi-gtdb_map.py
  • Map taxonomic classifications between the NCBI and GTDB taxonomies
  • Taxonomy mapping is done via the GTDB metadata table (includes both NCBI & GTDB taxonomies)
  • Mapping can go either way: NCBI => GTDB or GTDB => NCBI (see --query-taxonomy)
  • The user can select “fuzzy” mappings, in which the mapping isn’t a perfect 1-to-1
  • See the script help docs for examples on usage
• gtdb_to_diamond.py
  • Use to create a diamond database (with taxonomy) of genes from GTDB genomes
  • This can be used to taxonomically classify reads and amino acid sequences with diamond & GTDB
  • See the script help docs for examples on usage
• lineage2taxid.py
  • Use to get the taxids for a set of lineages (eg., from GTDB-Tk)
  • This is somewhat of a reverse of gtdb_to_taxdump.py
  • The script can work with GTDB or NCBI tax dumps
• acc2gtdb_tax.py
  • Use to create an accession2taxid file
  • Create sequence accession to TAXID mapping file
  • This will go through every GTDB genome, to get sequence accession, which will take a while.
• ./uniref_utils/
  • unirefxml2clust50-90idx.py
    • Mapping UniRef90 cluster IDs to UniRef50 cluster IDs
  • unirefxml2fasta.py
    • Creating gene sequence fasta from xml
  • unirefxml2tax.py
    • Converting the xml to a table of gene taxonomies

GTDB website

https://data.ace.uq.edu.au/public/gtdb/data/releases/