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 assembly process, the retrieved DENV reads are firstly assembled with SPAdes Genome 354 Assembler [15] with the options "-careful -only-assembler -cov-cutoff ". The coverage cutoff if 355 dictated by the "-spadesMinCoverage" and "-spadesMinKmerCoverage" parameters, set to 2 by 356 default. If the assembly with SPAdes fails to produce a contig equal or greater than the value 357 defined in the "-minimumContigSize" parameter (default of 10000), the data is re-assembled with the 358 MEGAHIT assembler [16] with default parameters. By default the k-mers to be used in the assembly 359 in both tools ("-spadesKmers" and "-megahitKmers") are automatically determined depending on 360 the read size. If the maximum read length is equal or greater than 175 nucleotides, the assembly is 361 done with the k-mers "55, 77, 99, 113, 127", otherwise the k-mers "21, 33, 55, 67, 77" are used.