MAB MLST Scheme for Mycobacterium absecssus

This repository contains a novel 15 gene MLST scheme for Mycobacterium absecssus.

Citation

Wuzinski M, Bak AK, Petkau A, Demczuk WH, Soualhine H, Sharma MK. A multilocus sequence typing scheme for Mycobacteriumabscessus complex (MAB‑multilocus sequence typing) using whole‑genome sequencing data. Int J Mycobacteriol 2019;8:273‑80. doi:10.4103/ijmy.ijmy_106_19.

Usage

Please see the Installation instructions below for how to get this scheme setup before continuing with the below steps.

Command-line MLST

To use this scheme with the mlst software, please do the following.

mlst --scheme mab_mabscessus input/*.fasta > output.txt

You will likely have to set the scheme explicitly --scheme mab_mabscessus as other schemes in PubMLST may match your input files. The final output file will look something like:

input/SRR6388757.fasta  mab_mabscessus  49  hsp(1)  erm(1)   rrl(1)  rrs(1)  arr(8)  argH(4)  cya(5)  gnd(1)  murC(2)  pta(10)  purH(2)  rpoB(1)  gyrA(8)   gyrB(7)   recA(9)
input/SRR6388758.fasta  mab_mabscessus  43  hsp(1)  erm(14)  rrl(1)  rrs(1)  arr(6)  argH(1)  cya(4)  gnd(3)  murC(2)  pta(2)   purH(4)  rpoB(1)  gyrA(15)  gyrB(14)  recA(1)

See the Installation documentation below for how to get this scheme installed.

Galaxy

To use this scheme with Galaxy and the Galaxy MLST Tool please set the scheme to mab_mabscessus and run the tool on your genomes.

1. Running the Tool

   

2. Output

   

Installation

Command-line MLST

To use with Torsten's mlst software please copy the contents of this repository to to db/pubmlst/ and run mlst/scripts/mlst-make_blast_db (see instructions at https://github.com/tseemann/mlst#adding-a-new-scheme). The scheme will be named mab_mabsecssus in the mlst software.

Finding the db/pubmlst/ directory

To find the db/pubmlst/ directory you can run mlst --help and look for the information on the --datadir option. For example:

mlst --help
...
PATHS
  --blastdb [X]     BLAST database (default '/home/CSCScience.ca/apetkau/miniconda3/envs/mlst/db/blast/mlst.fa')
  --datadir [X]     PubMLST data (default '/home/CSCScience.ca/apetkau/miniconda3/envs/mlst/db/pubmlst')

Here, I can see that the full path to db/pubmlst directory is /home/CSCScience.ca/apetkau/miniconda3/envs/mlst/db/pubmlst.

Installing the scheme

Once you've found the full path to db/pubmlst you can install the scheme with the following commands:

cd db/pubmlst/

git clone https://github.com/phac-nml/mab_mabscessus.git

../../scripts/mlst-make_blast_db

You can verify it's installed by running:

mlst --longlist|grep mab_mabscessus
mab_mabscessus  hsp     erm     rrl     rrs     arr     argH    cya     gnd     murC    pta     purH    rpoB    gyrA    gyrB    recA

Galaxy

To make use of this scheme using the Galaxy version of the MLST tool you can do the following.

1. Install MLST in Galaxy

Please install the Galaxy MLST Tool in Galaxy.

2. Install this MLST scheme

To install a new MLST scheme you will have to find the location that the MLST tool is installed using conda by Galaxy. By default, the Galaxy version of conda is in galaxy/database/dependencies/_conda (if this does not exist, please check the galaxy/config/galaxy.yml file for the location of conda).

Once you've found this directory, please first add the conda binary to your PATH and activate the conda environment containing MLST.

cd /path/to/galaxy/_conda/bin

# add bin/ directory to PATH containing conda
export PATH=`pwd`:$PATH

# Activate __mlst@2.15.1 environment (or whichever version got installed by Galaxy)
source activate __mlst@2.15.1

Now, change to the db/pubmlst directory that got installed by conda for the mlst program.

# cd to __mlst@2.15.1 or whichever version is installed in Galaxy
cd /path/to/galaxy/_conda/envs/__mlst@2.15.1/db/pubmlst

Now, you can install the MLST scheme:

git clone https://github.com/phac-nml/mab_mabscessus.git

# Make the new BLAST databases
../../scripts/mlst-make_blast_db

3. Verify scheme is installed

To verify the scheme is installed you can run the Galaxy MLST List tool:

You should see mab_mabscessus in the output if it is properly installed.