Antimicrobial resistance identification using ARIBA

Introduction

ARIBA is a tool that identifies antibiotic resistance genes. This tutorial will walk you through the analysis of the Neisseria gonorrhoeae data set used in the ARIBA paper:

ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads
Hunt M, Mather AE, Sánchez-Busó L, Page AJ, Parkhill J , Keane JA, Harris SR.
Microbial Genomics 2017. doi: 110.1099/mgen.0.000131
PMID: 29177089

Learning outcomes

By the end of this tutorial you can expect to be able to:

Download and prepare the standard AMR databases for use with ARIBA
Prepare your own database for use with ARIBA
Perform QC on input data and understand why QC is important
Run ARIBA on several samples to identify antibiotic resistance
Understand the different flags produced by ARIBA
Summarise ARIBA results for several samples
Query the AMR results produced by ARIBA
Use Phandango to visualise ARIBA results

Tutorial sections

This tutorial comprises the following sections:

Authors

This tutorial was created by Martin Hunt.

Running the commands from this tutorial

You can run the commands in this tutorial either directly from the Jupyter notebook (if using Jupyter), or by typing the commands in your terminal window.

Running commands on Jupyter

If you are using Jupyter, command cells (like the one below) can be run by selecting the cell and clicking Cell -> Run from the menu above or using ctrl Enter to run the command. Let's give this a try by printing our working directory using the pwd command and listing the files within it. Run the commands in the two cells below.



In [ ]:

    
pwd



In [ ]:

    
ls -l

Running commands in the terminal

You can also follow this tutorial by typing all the commands you see into a terminal window. This is similar to the "Command Prompt" window on MS Windows systems, which allows the user to type DOS commands to manage files.

To get started, select the cell below with the mouse and then either press control and enter or choose Cell -> Run in the menu at the top of the page.



In [ ]:

    
echo cd $PWD

Now open a new terminal on your computer and type the command that was output by the previous cell followed by the enter key. The command will look similar to this:

cd /home/manager/pathogen-informatics-training/Notebooks/ARIBA/

Now you can follow the instructions in the tutorial from here.

Let’s get started!

This tutorial assumes that you have ARIBA installed on your computer. For download and installation instructions, please see the ARIBA GitHub-page.

To check that you have installed the software correctly, you can run the following command:



In [ ]:

    
ariba --help

This should return the following help message:

usage: ariba <command> <options>

ARIBA: Antibiotic Resistance Identification By Assembly

optional arguments:
  -h, --help      show this help message and exit

Available commands:

    aln2meta      Converts multi-aln fasta and SNPs to metadata
    expandflag    Expands flag column of report file
    flag          Translate the meaning of a flag
    getref        Download reference data
    micplot       Make violin/dot plots using MIC data
    prepareref    Prepare reference data for input to "run"
    pubmlstget    Download species from PubMLST and make db
    pubmlstspecies
                  Get list of available species from PubMLST
    refquery      Get cluster or sequence info from prepareref output
    run           Run the local assembly pipeline
    summary       Summarise multiple reports made by "run"
    test          Run small built-in test dataset
    version       Get versions and exit

To get started with the tutorial, head to the first section: How to use custom reference data with ARIBA