https://github.com/snitkin-lab-umich/ariba_snakemake
Snakemake pipeline to run ARIBA on genomes using CARD, PlasmidFinder, or MLST database
https://github.com/snitkin-lab-umich/ariba_snakemake
Last synced: about 2 months ago
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Snakemake pipeline to run ARIBA on genomes using CARD, PlasmidFinder, or MLST database
- Host: GitHub
- URL: https://github.com/snitkin-lab-umich/ariba_snakemake
- Owner: Snitkin-Lab-Umich
- Created: 2020-06-25T15:45:13.000Z (almost 5 years ago)
- Default Branch: master
- Last Pushed: 2020-09-08T14:10:03.000Z (over 4 years ago)
- Last Synced: 2025-01-26T17:36:09.882Z (4 months ago)
- Language: Shell
- Homepage:
- Size: 22.5 KB
- Stars: 0
- Watchers: 2
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# Snakemake pipeline to run ARIBA on genomes using CARD, PlasmidFinder, or MLST database
Written by Sophie Hoffman & Zena Lapp.
## Useful links
ARIBA, CARD, PlasmidFinder & MLST:
- [ARIBA wiki](https://github.com/sanger-pathogens/ariba/wiki)
- [CARD website](https://card.mcmaster.ca/)
- [PlasmidFinder website](https://cge.cbs.dtu.dk//services/PlasmidFinder/instructions.php)
- [MLST github](https://github.com/sanger-pathogens/ariba/wiki/MLST-calling-with-ARIBA)
[Snakemake setup](https://github.com/Snitkin-Lab-Umich/Snakemake_setup)
## Download this repo
First, go to the directory where you want to dowload the repo to. Next, run the following command:
```
git clone https://github.com/Snitkin-Lab-Umich/ariba_snakemake
```
## Snakemake and Conda
Visit this guide to [snakemake setup](https://github.com/Snitkin-Lab-Umich/Snakemake_setup) (including conda) to get started.
To create and activate the conda environment:
```
conda env create -f config/env.yaml # you only have to do this once
conda activate ariba # you have to do this every time
```
## Running the ARIBA snakemake pipeline on the cluster
To run the ARIBA snakemake pipeline on the cluster, you have to:
- Modify your email address in `ariba.sbat` and `config/cluster.yaml`
- Modify the fastq file directory path, and potentially the fastq file R1 suffix in the `snakefile`
- Choose which database (CARD, PlasmidFinder, or MLST) you want to run, and modify the `db_dir` path to match the location of that database
Then run:
```
conda activate ariba # if you're not already in the ariba conda environment
sbatch ariba.sbat
```
You can check your job using:
```
squeue -u UNIQNAME
```
The pipeline outputs:
- An `ariba` directory with a subdirectory for each input genome containing the ARIBA results
- Two summary files (the most useful output, in my opinion):
- `results/ariba_minimal_results.csv` (contains presence/absence, i.e. match, results from ARIBA output)
- `results/ariba_all_results.csv` (contains comprhensive results from ARIBA output, i.e. the following columns for each gene: assembled,match,ref_seq,pct_id,ctg_cov,known_var,novel_var)