https://github.com/artoria2e5/gtdb-treebase

Script for converting a GTDB database to a treebase format in opentreeoflife.
https://github.com/artoria2e5/gtdb-treebase

Last synced: 14 days ago
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Script for converting a GTDB database to a treebase format in opentreeoflife.

• Host: GitHub
• URL: https://github.com/artoria2e5/gtdb-treebase
• Owner: Artoria2e5
• License: cc0-1.0
• Created: 2021-02-05T08:20:11.000Z (over 4 years ago)
• Default Branch: main
• Last Pushed: 2021-02-05T11:27:14.000Z (over 4 years ago)
• Last Synced: 2025-02-17T15:52:14.805Z (3 months ago)
• Language: Python
• Size: 7.81 KB
• Stars: 0
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# GTDB-Treebase

Script for converting a GTDB database to a treebase format in opentreeoflife.

## What we do now

* Map representative genomes to species

* Map suffixed genus names in species to conventional versions

* Trim off the taxon level prefix – Actually we can do it in the mapper

* Join up bacteria and archaea at a root for single-file upload

## Why some stuff aren't done yet

### More to conventional (NCBI) names

In theory we could use the `auxillary_files/gtdb_vs_ncbi_*.xlsx` to do a deeper species

mapping, but that is quite risky. Mapping on the higher-level taxa feels pointless too.

## Stuff I really should do

* Instead of the taxonomy tsv, fetch the data from GenBank directly. In other words,

  erase GTDB taxonomy and just use the hot mess. Will make OTU mapping a lot smoother...