DEN-IM: Dengue Virus identification from shotgun and targeted metagenomics

C I Mendes; E Lizarazo; M P Machado; D N Silva; A Tami; M Ramirez; N Couto; J W A Rossen; J A Carriço

• The HTML reports obtained with DEN-IM can be easily shared, facilitating comparison of results from across the globe. Figure 1 . The DEN-IM workflow separated into five different components. The raw sequencing reads are provided as input to the first block (in blue), responsible for quality control and elimination of low-quality reads and sequences. After successful pre-processing of the reads, these enter the second block (green) for retrieval of the DENV reads using the mapping database of 3830 complete DENV genomes as reference. This block also provides an initial estimate of the sequencing depth. After the de novo assembly and assembly correction block (yellow), the coding sequences (CDSs) are retrieved and are then classified with the reduced complexity DENV typing database containing 161 sequences representing the known diversity of DENV serotypes and genotypes (red).If a complete CDS fails to be assembled, the reads are mapped against the DENV typing database and a consensus sequence is obtained for classification and phylogenetic inference. All CDSs are aligned and compared in a phylogenetic analysis (purple). Lastly, a report is compiled (gray) with the results of all the blocks of the workflow. Figure S1 ).