patho_typing

In silico pathogenic typing pathogenic directly from raw Illumina reads

https://github.com/B-UMMI/patho_typing

Requirements

• Fastq file

Dependencies

• ReMatCh >= v3.2 (https://github.com/B-UMMI/ReMatCh)

Installation

git clone https://github.com/B-UMMI/patho_typing.git

Usage

usage: patho_typing.py [-h] [--version] -f /path/to/input/file.fq.gz
                       [/path/to/input/file.fq.gz ...] -s Yersinia
                       enterocolitica [-o /path/to/output/directory/] [-j N]
                       [--trueCoverage] [--noCheckPoint] [--minGeneCoverage N]
                       [--minGeneIdentity N] [--minGeneDepth N]
                       [--doNotRemoveConsensus] [--debug]

In silico pathogenic typing directly from raw Illumina reads

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

Required options:
  -f /path/to/input/file.fq.gz [/path/to/input/file.fq.gz ...], --fastq /path/to/input/file.fq.gz [/path/to/input/file.fq.gz ...]
                        Path to single OR paired-end fastq files. If two files
                        are passed, they will be assumed as being the paired
                        fastq files (default: None)
  -s Yersinia enterocolitica, --species Yersinia enterocolitica
                        Species name (default: None)

General facultative options:
  -o /path/to/output/directory/, --outdir /path/to/output/directory/
                        Path to the directory where the information will be
                        stored (default: .)
  -j N, --threads N     Number of threads to use (default: 1)
  --trueCoverage        Assess true coverage before continue typing (default:
                        False)
  --noCheckPoint        Ignore the true coverage checking point (default:
                        False)
  --minGeneCoverage N   Minimum typing percentage of target reference gene
                        sequence covered to consider a gene to be present
                        (value between [0, 100]) (default: None)
  --minGeneIdentity N   Minimum typing percentage of identity of reference
                        gene sequence covered to consider a gene to be present
                        (value between [0, 100]). One INDEL will be considered
                        as one difference (default: None)
  --minGeneDepth N      Minimum typing gene average coverage depth of present
                        positions to consider a gene to be present (default
                        15, or 1/3 of average sample coverage assessed by true
                        coverage analysis) (default: None)
  --doNotRemoveConsensus
                        Do not remove ReMatCh consensus sequences (default:
                        False)
  --debug               DeBug Mode: do not remove temporary files (default:
                        False)

Outputs

run.*.log
ReMatCh running log file.

patho_typing.report.txt
List with possible pathotypes found.

ReMatCh folder
For each ReMatCh run (typing and trueCoverage, the latter when required), the rematchModule_report.txt is kept.

• rematchModule_report.txt - Report file containing gene information: 1) gene name, 2) percentage of target gene sequence covered, 3) Mean target gene coverage depth of present positions, 4) percentage of target gene sequence with lower coverage depth, 5) number of positions in target gene sequence containing multiple alleles, 6) percentage identity of target gene sequence covered. The general sample information will also be stored: number of absent genes, number of genes with multiple alleles among the genes present and the mean sample coverage depth (only considering the genes present).

Contact

Miguel Machado
mpmachado@medicina.ulisboa.pt