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

In order to recover the maximum number of DENV reads from the input HTS data in the first 307 mapping step (Figure 1) , we maintained the database with the 3830 complete DENV genomes to 308 retain as much diversity as possible. This database is referred as "DENV mapping database". (Table S4) , 63 DENV-2 (Table S5) , 25 DENV-3 (Table S6 ) and 27 DENV-4 (Table S7 ). This database 313 is referred as "DENV typing database". This step is necessary to speed up the classification step for (Table S4 ). In order to harmonise dengue nomenclature, the 324 system adopted uses Roman-numeric labels to identify the genotype, with the exception of Serotype 325 2 (Table S5) , which used both Roman-numeric and geographic origin due to the widespread adoption 326 of the latter. The short-read paired-end data is passed as input through the "-fastq" parameter, that by default 329 is set to match all files in the "fastq" folder that match the pattern "* R1,2* ". In the process to 330 verify the integrity of the paired-end raw sequencing data, the integrity of the input files is assessed 331 by attempting to decompress and read the files. An estimation of the depth of coverage is also 332 performed. By default, the input size ("-genomeSize") is set to 0.012 Mb and the minimum coverage 333 depth ("-minCoverage") is set to 10. If any input file is found to be corrupt, its progression in the 334 workflow is aborted.