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 the FastQC and Trimmomatic module, FastQC (https://www.bioinformatics.babraham. 336 ac.uk/projects/fastqc/) is run with the parameters "-extract -nogroup -format fastq". FastQC 337 will inform Trimmomatic [10] on how many bases to trim from the 3'and 5' ends of the raw reads. The removal of low complexity sequences is done with PrinSeq [12] using a custom parameter 343 ("-pattern"), which by default is set to the value "A 50%; T 50%; N 50%", removing sequences whose To retrieve the reads that map to the DENV reference database, Bowtie2 [13] is run with default parameters with the DENV mapping database as a reference. The reads and their mates that map 347 to the reference are retrieved with "samtools view -buh -F 12 " and "samtools fastq" commands.