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 serotyping and genotyping is performed with the Seq Typing tool [18] with the command 374 "seq typing.py assembly" or "seq typing.py reads", using as reference the provided curated DENV 375 typing database. It is possible to retrieve the genomes of the closest references and include them in The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/628073 doi: bioRxiv preprint a) b) Figure S1 . a) DEN-IM's quality control report containing information of the number of basepairs and the number of reads for the analysed samples, the estimated coverage depth before and after mapping, and the percentage of reads in the input data that were trimmed. b)DEN-IM's typing report for 24 CDSs recovered from the metagenomic dataset. The ID contains the CDS contig name, the typing result for serotype-genotype, the values for identity and coverage, and the GenBank ID of the closest reference in the Typing Database containing 161 complete DENV genomes. The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/628073 doi: bioRxiv preprint Figure S2 . Maximum Likelihood inference of the multiple sequence alignment of the 46 DENV-1 complete genomes in the typing dataset. 1635 complete DENV-1 genomes were clustered at 98% nucleotide identity and the representative genomes were aligned with mafft. A maximum likelihood tree was infered with RAxML. The tree is coloured according to genotype (red: genotype I; green: genotype II; blue: genotype III; purple: genotype IV). The sample JF459993, marked with a star, is currently annotated in ViPR as belonging to genotype IV but, given to the good phylogenetic support, it was re-classified as belonging to the genotype I. .