Abricate Genomes

Identify some fun stuff in a slew of genomes

This is a simple wrapper for Torsten's ABRicate to generate a .csv (please forgive me Torsten) that concatenates all virulence factors found among the eight databases that can be searched with ABRicate.

Quick Start

git clone https://github.com/greenkidneybean/abricate_genomes.git
cd abricate_genomes
conda create --name abricate_env --file env/abricate_linux.txt
python abricate_genomes.py samples.csv

Setup

1. Clone this repo

git clone https://github.com/greenkidneybean/abricate_genomes.git

2. Install Miniconda, here's a guide for setup on Biowulf
3. Create the abricate_env conda environment:

conda create --name abricate_env --file abricate_linux.txt

Input

Takes a .csv file with two columns: "samples" and "path". Check-out the samples.csv file as a guide for formating the sample input.

sample,path
sample_1,test/sample_1.fa
sample_2,test/sample_2.fa
sample_3,test/sample_3.fa

Output

The abricate_genomes.py file will generate a new directory titled "abricate" containing a pile of files. The primary output file of interest is the abricate/abricate.csv, which flattens the results of each sample summary.csv into a single line. A zero (0) indicates that the virulence factor was not found in any of the eight databases. A one (1) indicates that the virulence factor was found in at least one of the eight databases.

abricate
├── abricate.csv                # summary file of virulence factors
├── fig                         # sample heatmaps with database hits
│   ├── sample_1.png
│   ├── sample_2.png
│   └── sample_3.png
└── samples
    ├── sample_1                # database.out for each database
    │   ├── argannot.out
    │   ├── card.out
    │   ├── ecoh.out
    │   ├── ecoli_vf.out
    │   ├── ncbi.out
    │   ├── plasmidfinder.out
    │   ├── resfinder.out
    │   ├── summary.csv         # summary table of percent hit in each database
    │   ├── summary.tab         # summary table of percent hit in each database
    │   └── vfdb.out
    └── ...

Run

# activate the "abricate_env" conda environment
conda activate abricate_env

# check the very mild help flag for script options
python abricate_genomes.py -h

# run abricate_genomes.py with the provided test data
python abricate_genomes.py samples.csv