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Dengue virus genotyping from shotgun and targeted metagenomics​ - A nextflow pipeline
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README.md

DEN-IM

DEN-IM_logo

DEN-IM is a one-stop, user-friendly, containerised and reproducible workflow for the analysis of DENV sequencing data, both from shotgun and targeted metagenomics approaches. Is is able to infer DENV coding sequence (CDS), identify serotype and genotype, and generate a phylogenetic tree.

As input DEN-IM accepts raw Illumina sequencing reads, and and informs the user with an interactive HTML report with information on the quality control, mapping, assembly typing and phylogenetic analysis, as well as all the output files of the whole pipeline.

It is implemented in Nextflow, a workflow management system that allows the effortless deployment and execution of complex distributed computational workflows. DEN-IM integrates Docker containerised images for all the tools necessary for its execution, ensuring reproducibility and the tracking of both software code and version, regardless of the operating system used.

Installation

Before installing DEN-IM, a few dependencies must be installed in your system:

  • Nextflow

Nextflow (version 0.31.0 or higher) can be used on any POSIX compatible system (Linux, OS X, etc). It requires BASH and Java 8 (or higher) to be installed. More instructions are available here.

  • Container Engine

All components of DEN-IM are executed in docker containers, which means that you’ll need to have a container engine installed. The container engines available are the ones supported by Nextflow:

If you already have any one of these installed, you are good to go as the provided docker containers are compatible with all engines available. If not, you’ll need to install one.

  • Local Instalation

A local installation of DEN-IM is also required as Nextflow's pipeline sharing is not compatible with DEN-IM's architecture. You can clone this repository with git clone https://github.com/B-UMMI/DEN-IM.git, and all files will be in your local machine.

Running DEN-IM

After you have a local installation of DEN-IM, you can get started using the workflow with:

single-end reads: nextflow run DEN-IM.nf --fastq="/path/to/input/files/*.fq.gz"

paired-end reads: nextflow run DEN-IM.nf --fastq="/path/to/input/files/*_{1,2}.fq.gz"

By default nextflow executes DEN-IM with singularity, but this can be changed by adding -pofile docker to the command.

Users can customize the workflow execution either by using command line options or by modifying a simple plain-text configuration file (params.config), where parameters are set as key-value pairs. The version of tools used can also be changed by providing new container tags in the appropriate configuration file (containers.config), as well as the resources for each process (resources.config).

More information on how to personalize the config files can be found in the wiki.

Output and Report

The output files are stored in the results/ folder in the directory where the workflow was executed. The nextflow log file for the execution of the pipeline can be found in the directory of execution. Log files for each of the components in the workflow are stored inside the results/ folder. DEN-IM creates an interactive HTML report, stored in the pipeline_results/ folder in the directory where the workflow was executed. To open the report simply click oh the pipeline_report.html file and the report will open on your default browser.

Citation and Contacts

DEN-IM was developed by the Molecular Microbiology and Infection Unit, at Instituto de Medicina Molecular, in collaboration with Personalised Microbiology Lab at UMCG. A pre-print is available at biorxiv.

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