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Inês Mendes edited this page May 5, 2020 · 19 revisions

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DEN-IM (Dengue Virus Identification from Metagenomic and Targeted Sequencing) is an automated Nextflow-based workflow enabling the identification, serotyping, genotyping, and phylogenetic analysis of DENV data, both from shotgun and targeted metagenomics approaches. It is able to infer DENV coding sequence (CDS), identify serotype and genotype, and generate a phylogenetic tree. It can easily be run any UNIX-like system, from local machines to high-performance computing clusters, performing a comprehensive analysis without the requirement of extensive bioinformatics expertise.

As input DEN-IM accepts raw paired-end 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. Due to it's Nextflow implementation, it allows 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 in a tutorial-like fashion on how to run the DEN-IM workflow can be found in the How to Run DEN-IM Workflow page, including how to set the parameters in the nextflow config files. It also includes information on how to personalize resources and container images for DEN-IM execution. Alternatively, you can have a look at the shorter TL;DR! instructions!

  • Information on DEN-IM's output files and report is available in the Output and Report section.

DEN-IM is available as a pre-print on biorxiv! The results for the two datasets analysed are available in the Shotgun and a Targeted metagenomics datasets section.

DEN-IM is now published at Microbial Genomics! If you use it, please cite: Mendes CI, Lizarazo E, Machado MP, Silva DN, Tami A, Ramirez M, et al. DEN-IM: dengue virus genotyping from amplicon and shotgun metagenomic sequencing. Microb Genomics. 2020 Mar 5; Available from: https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000328

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

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