In silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST).

• Jason Kwong (@kwongjc)
• Anders Gonçalves da Silva
• Torsten Seemann (@torstenseemann)

• Python >= 3.6
• BioPython
• isPcr >=v33x2 by Jim Kent

The easiest way of installing ngmaster is using pip:

$ pip3 install --user git+https://github.com/MDU-PHL/ngmaster.git

The --user option will install the package locally, rather than in the global python directory.

Thus, by default, this will install the package in $HOME/.local/, and the executable in $HOME/.local/bin/. To install the executable in a custom location (e.g., $HOME/bin), use the following:

$ pip3 install --install-option="--install-scripts=$HOME/bin" --user git+https://github.com/MDU-PHL/ngmaster.git

To upgrade to a newer version:

$ pip3 install --upgrade --install-option="--install-scripts=$HOME/bin" --user git+https://github.com/MDU-PHL/ngmaster.git

The simplest way to install dependencies is to use the Brew (Mac OS X) or LinuxBrew (Linux) system. Users who have difficulty installing isPcr from source (eg. Mac OS) may have more success with Brew:

$ brew tap homebrew/science
$ brew tap chapmanb/cbl
$ brew tap tseemann/homebrew-bioinformatics-linux

Once installed, you can run the following to ensure ngmaster is successfully working:

$ ngmaster --test

If everything works, you will see the following:

Running ngmaster.py on test example (NG-MAST 10699) ...
$ ngmaster.py test/test.fa
ID    NG-MAST    POR    TBPB
test.fa    10699    6277    4
... Test successful.

$ ngmaster -h
    
usage: 
  ngmaster [OPTIONS] <fasta1> <fasta2> <fasta3> ... <fastaN>

In silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST)

Please cite as:
  Kwong JC, Goncalves da Silva A, Howden BP and Seemann T.
  NGMASTER: in silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST)
  GitHub: https://github.com/MDU-PHL/ngmaster

positional arguments:
  FASTA            input FASTA files eg. fasta1, fasta2, fasta3 ... fastaN

optional arguments:
  -h, --help       show this help message and exit
  --db DB          specify custom directory containing allele databases
                   directory must contain database files "POR.tfa", "TBPB.tfa", and "ng_mast.txt"
  --csv               output comma-separated format (CSV) rather than tab-separated
  --printseq FILE  specify filename to save allele sequences to (default=off)
   --updatedb       update allele database from <www.ng-mast.net>
  --test           run test example
  --version        show program's version number and exit

To perform in silico NG-MAST on FASTA files:

$ ngmaster <fasta1> <fasta2> <fasta3> ... <fastaN>

The NG-MAST result and allele numbers are printed in tab-separated format to stdout.

• If an allele is not found (ie. unable to located with primers), the allele result is "–".
• If an allele is found (ie. located with primers), but the conserved region containing the starting key motif required for sequence trimming cannot be located, the allele result is "no_key".
• If an allele is found (ie. located with primers), but the trimmed sequence is novel, and not in the current database, the allele result is "new".

To save results to a tab-separated text file, redirect stdout:

$ ngmaster <fasta1> <fasta2> <fasta3> ... <fastaN> > results.txt

To display results in comma-separated format, use the --csv option:

$ ngmaster --csv <fasta1> <fasta2> <fasta3> ... <fastaN>

To save sequences of the alleles to a file (eg. for uploading "new" sequences to http://www.ng-mast.net):

$ ngmaster --printseq [filename] <fasta1> <fasta2> <fasta3> ... <fastaN>

To update the allele databases from http://www.ng-mast.net :
Warning: This will overwrite the existing databases so ensure you back them up if you wish to keep them.

$ ngmaster.py --updatedb

A copy of the old database is saved just in case, but is overwritten with each subsequent --updatedb.

To update the allele databases into a different folder (ie. not the /db folder in the ngmaster directory):

$ ngmaster.py --updatedb --db path/to/folder

This will download the database files into the folder path/to/folder. This can then be specified when running ngmaster using the --db path/to/folder option.

1. Create custom database files: POR.tfa, TBPB.tfa, ng_mast.txt
   See default db directory for examples.
   POR.tfa and TBPB.tfa contain the respective allele sequences in FASTA format.
   ng_mast.txt contains a list of NG-MAST types and the corresponding allele types.

2. Place the custom database files in a folder.

3. Specify the path to that custom database folder:
   $ ngmaster --db [/path/to/custom/folder/] <fasta1> <fasta2> <fasta3> ... <fastaN>

Please cite as:

Kwong JC, Gonçalves da Silva A, Dyet K, Williamson DA, Stinear TP, Howden BP and Seemann T.
NGMASTER: in silico multi-antigen sequence typing for Neisseria gonorrhoeae.
Microbial Genomics 2016; doi: 10.1099/mgen.0.000076

Please submit via the GitHub issues page.

Note that the NG-MAST databases and website are curated and hosted at the Department of Infectious Disease Epidemiology, Imperial College London. For issues with the NG-MAST databases, please contact the NG-MAST curator.

GPLv2

• Martin et al. J Infect Dis, 2004 Apr 15; 189(8): 1497-1505.
• See also http://www.ng-mast.net.