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Martin RETHORET-PASTY's avatar
Adding last database (04-03)
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README.md

diphtOscan

diphtOscan is a command line script written in Python. DiphtOscan runs on UNIX, Linux and most OS X operating systems. For more details, see the associated publication (https://www.biorxiv.org/content/10.1101/2023.02.20.529124v1xxx).

diphtOscan is a tool to search genomic assemblies of Corynebacterium diphtheriae and other species of the Corynebacterium diphtheriae species complex (CdSC) for:

  • Species (e.g. C. diphtheriae, C. ulcerans, C. pseudotuberculosis, C. belfantii, C. rouxii , C. ramonii and C. silvaticum)
  • Biovar-associated genes (spuA, nitrate reductase gene cluster)
  • MLST sequence type
  • Virulence factors, including tox gene detection and disruption prediction
  • Antimicrobial resistance determinants: acquired genes (ermX, pbp2m, …) and SNPs (e.g., rpoB, gyrA)
  • Genomic context of genomic features associated with resistance
  • Presence of integrons (using Integron Finder: https://github.com/gem-pasteur/Integron_Finder)
  • Tree building (using JolyTree: https://gitlab.pasteur.fr/GIPhy/JolyTree)

Installation and execution

A. Install the following programs and tools, or verify that they are already installed with the required version:

Note: Need for the --tree i.e. using the Jolytree tool (https://gitlab.pasteur.fr/GIPhy/JolyTree)

  • Jolytree version >= 2.1 (The JollyTree repository should be cloned into diphtoscan/script/)

Need for the --integron i.e. using the Integron Finder version 2 tool (https://github.com/gem-pasteur/Integron_Finder)

B. Clone this repository with the following command line:

git clone https://gitlab.pasteur.fr/BEBP/diphtoscan.git

C. Give the execute permission to the file diphtoscan/__main__.py:

chmod +x diphtoscan/__main__.py

D. Run the installation of the JollyTree module (if you plan to use it) :

diphtoscan/script/update_tools.sh

E. Execute diphtOscan with the following command line model:

python __main__.py [options]

Usage

Launch diphtOscan without option to read the following documentation:

usage: __main__.py -a ASSEMBLIES [ASSEMBLIES ...] [-u] [-st] [-t] [-res_vir] [-plus] [-integron] [-o OUTDIR]
                   [--min_identity MIN_IDENTITY] [--min_coverage MIN_COVERAGE] [--threads THREADS] [-tree] 
                   [--overwrite] [-h] [--version]

diphtOscan: a tool for characterising virulence and resistance in Corynebacterium

Updating option:
  -u, --update          Update database MLST, Tox Allele & AMR (default: no).The database update can be executed on its own without the -a option.

Required arguments:
  -a ASSEMBLIES [ASSEMBLIES ...], --assemblies ASSEMBLIES [ASSEMBLIES ...]
                        FASTA file(s) for assemblies.

Screening options:
  -st, --mlst           Turn on species Corynebacterium diphtheriae species complex (CdSC) and MLST sequence type
                        (default: no)
  -t, --tox             Turn on tox allele (default: no)
  -res_vir, --resistance_virulence
                        Turn on resistance and virulence genes screening (default: no resistance and virulence gene
                        screening)
 
  -plus, --extend_genotyping
                        Turn on all virulence genes screening (default: no all virulence gene screening)
  -integron, --integron
                        Screening the intregon(default: no)

Output options:
  -o OUTDIR, --outdir OUTDIR
                        Folder for detailed output (default: results_YYYY-MM-DD_II-MM-SS_PP)

Settings:
  --min_identity MIN_IDENTITY
                        Minimum alignment identity for main results (default: 80)
  --min_coverage MIN_COVERAGE
                        Minimum alignment coverage for main results (default: 50)
  --threads THREADS     The number of threads to use for processing. (default: 4)
  --overwrite           Allows the output directory to be overwritten if it already exists

Phylogenetic tree:
  -tree, --tree         Generates a phylogenetic tree from JolyTree

Help:
  -h, --help            Show this help message and exit
  --version             Show program's version number and exit

Example

In order to illustrate the usefulness of diphtOscan and to describe its output files, the following use case example describes its usage for inferring a phylogenetic tree of Corynebacterium diphtheriae genomes derived from the analysis of Hennart et al.

Running diphtOscan

The following command line allows the script diphtOscan to be launched with default options on 8 threads:

python3 __main__.py -a $genomes --mlst --resistance_virulence --threads 8 -o Cdiphteriae

As the basename was set to 'Cdiphteriae', diphtOscan writes in few minutes the four following output files:

  • Cdiphteriae.csv: result file
  • $strain.fa: extracted sequences (for every assemblie files)
  • $strain.out: BLAST output file (for every assemblie files)