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Antibiotic Resistant Gene (ARG) Identifier

A workflow that accelerates identification of ARG-like sequences with CARD RGI. Built and tested on GNU/Linux.

Steps

  1. Filter fasta sequences for those that contain possible ARGs
  2. Run RGI against the filtered fasta file
  3. Create fasta file for each ARO with all predicted ARGs

Usage

Usage: runner.py [OPTIONS] CONTIGS_FASTA

  Analysis Workflow Management

  Sets up Pyflow WorkflowRunner and launches locally by default or via flux

Options:
  -r, --reference TEXT
  -o, --output TEXT
  --flux / --no-flux
  --dispatch / --no-dispatch
  -a, --account TEXT
  -p, --ppn INTEGER
  -m, --mem TEXT
  -w, --walltime TEXT
  --help                      Show this message and exit.

Install anaconda environment and dependencies

$ git clone https://github.com/jordangumm/arg_identifier.git
$ cd arg_identifier && ./build.sh

Run workflow

$ source ./dependencies/miniconda/bin/activate
$ python runner.py [CONTIGS_FASTA]

Run workflow on Flux

Depending on the size of the input fasta and/or reference, you may need to increase the memory --mem and processor count --ppn

$ source ./dependencies/miniconda/bin/activate
$ python runner.py [CONTIGS_FASTA] --flux --account [ACCOUNT]