https://github.com/metagenome-atlas/snake_gtdbtk

A snakemake for GTDB-tk
https://github.com/metagenome-atlas/snake_gtdbtk

Last synced: 11 days ago
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A snakemake for GTDB-tk

• Host: GitHub
• URL: https://github.com/metagenome-atlas/snake_gtdbtk
• Owner: metagenome-atlas
• Created: 2022-10-24T14:04:02.000Z (about 2 years ago)
• Default Branch: main
• Last Pushed: 2023-08-31T09:27:07.000Z (about 1 year ago)
• Last Synced: 2024-11-02T15:02:47.040Z (15 days ago)
• Language: Python
• Size: 11.7 KB
• Stars: 5
• Watchers: 1
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# GTDB-tk Snakemake Workflow

It uses GTDB-tk to taxonomically annotate your genomes and to build a tree.

Run as follows:

```

dbdir="databases"

genome_dir="genomes"

snakemake --use-conda --conda-prefix "$dbdir/conda_envs" \

 --config database_dir="$dbdir" genome_dir="$genome_dir"

```

where `dbdir` is the path to a (shared) directory to place the GTDB database and conda envs.

`genome_dir` should be the folder containing all genome fastas.

This code was developped as part of [metagenome-atlas](https://github.com/metagenome-atlas/atlas). 

Don't forget to cite the [GTDB-tk](https://github.com/Ecogenomics/GTDBTk)