patho_typing

In silico pathogenic typing directly from raw Illumina reads

---

• Rational
• Input requirements
• Dependencies
  • Install dependencies
• Install patho_typing
• Usage
• Outputs
• Citation
• Contact

Rational

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patho_typing is a tool for in silico pathogenic typing sample's reads through a read mapping approach using a set of reference sequences and defined rules for sequences presence/absence.
Sample's reads are mapped to the given reference sequences using Bowtie2, parsed with Samtools and analysed via ReMatCh. Based on the length of the sequence covered, it's depth of coverage and sequence nucleotide identity, patho_typing scores those for presence or absence, following defined thresholds. According to the combination of sequences present, a pathotype is returned following a set of rules for sequences presence/absence. Some of the sequences can be either present or absent. Reference sequences definition and presence/absence rules delineation are required pathotyping classification.

Input requirements

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• Fastq file

Dependencies

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• Python 3
• ReMatCh

Install dependencies

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ReMatCh:

git clone https://github.com/B-UMMI/ReMatCh.git
cd ReMatCh
python3 setup.py install

NOTE:
If you don't have permission for global system installation, try the following install command instead:
python3 setup.py install --user

Install patho_typing

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git clone https://github.com/B-UMMI/patho_typing.git
cd patho_typing
python3 setup.py install

NOTE:
If you don't have permission for global system installation, try the following install command instead:
python3 setup.py install --user

Usage

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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

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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).

Citation

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MP Machado, J Halkilahti, M Pinto, JP Gomes, M Ramirez, M Rossi, JA Carrico. patho_typing GitHub https://github.com/B-UMMI/patho_typing

Contact

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Miguel Machado
mpmachado@medicina.ulisboa.pt