MLST pipeline

by Judith Bergadà Pijuan

This pipeline is aimed to perform the assembly and annotation of paired-end sequencing reads, as well as to scan the resulting contig files against PubMLST typing schemes. Given multiple paired-end sequencing reads (FASTQ files), it provides a tab-separated table showing the matching PubMLST per paired-files, their ST (sequence type), and their allele IDs. It also provides the de novo assembly of the sequencing reads and their annotation.

Installation

To use this pipeline, you need to install the following dependencies:

• SPAdes
• MLST
• Prokka
• Agat (only if a GTF file is needed)

Later, you need to download the tool:

cd $HOME
git clone https://github.com/judithbergada/Pipeline_MLST

Usage

The pipeline expects you to have the following folder:

• FASTQ folder: this is a folder containing only your sequencing reads (FASTQ files). You must have all your FASTQ files here, and it is important that the pairs of files have the same prefix in the name.

To get information about the usage, please try:

./mlstpipeline.sh -h

The MLST tool can be used with these parameters:

Usage: mlstpipeline.sh    [-h or --help]
                          [-f or --fastqfolder]
                          [-o or --outname]
                          [-t or --threads]
                          [-c or --conversion]

Optional arguments:
    -h, --help:
                Show this help message and exit.
    -o, --outname:
                Name of your analysis.
                It will be used to name the output files.
                Default: mymlst.
    -t, --threads:
                Number of threads that will be used.
                It must be an integer.
                Default: 8.
    -c, --conversion:
                If required, create a GTF annotation file.
                Default: create only the default annotation files from Prokka.
Required arguments:
    -f, --fastqfolder:
                Path to the folder that contains ALL your FASTQ files.
                Only FASTQ files should be placed in it.
                You need forward and reverse paired-end reads.

Enjoy using the tool!