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Welcome to the DEN-IM wiki.

DEN-IM (Dengue Virus Identification from Metagenomic and Targeted Sequencing) is a ready-to-use bioinformatic analysis workflow for the processing and phylogenetic analysis of DENV using paired-end Illumina raw sequencing data.

It's built in nextflow, allowing out of the box high-level parallelization so it can be executed on any UNIX-like system, from local machines to high-performance computing facilities.

For installation instructions, visit the Getting Started section or the README page in the GitHub project.

Easy to follow instructions on how to run the DEN-IM workflow can be found in the How to Run DEN-IM page, including a tutorial on how to set the parameters in the nextflow.config file, and describe the files that will be produced in output. Alternatively, you can have a look at the TL;DR instructions!

To personalize DEN-IM's container technology, you can follow the How to use Docker, and the How to use Singularity tutorial. If you are using an HPC facility, please refer to How to run DEN-IM on a HPC section. For Amazon Web Services (AWS) instructions, refer to the How to run DEN-IM on AWS page.

Any issues, comments or concerns please visit the GitHub Issues page or contact us at [email protected]