DEN-IM: dengue virus genotyping from amplicon and shotgun metagenomic sequencing

Microbial Genomics
C I MendesJ. A. Carrico

Abstract

Dengue virus (DENV) represents a public health threat and economic burden in affected countries. The availability of genomic data is key to understanding viral evolution and dynamics, supporting improved control strategies. Currently, the use of high-throughput sequencing (HTS) technologies, which can be applied both directly to patient samples (shotgun metagenomics) and to PCR-amplified viral sequences (amplicon sequencing), is potentially the most informative approach to monitor viral dissemination and genetic diversity by providing, in a single methodological step, identification and characterization of the whole viral genome at the nucleotide level. Despite many advantages, these technologies require bioinformatics expertise and appropriate infrastructure for the analysis and interpretation of the resulting data. In addition, the many software solutions available can hamper the reproducibility and comparison of results. Here we present DEN-IM, a one-stop, user-friendly, containerized and reproducible workflow for the analysis of DENV short-read sequencing data from both amplicon and shotgun metagenomics approaches. It is able to infer the DENV coding sequence (CDS), identify the serotype and genotype, and generate a phyloge...Continue Reading

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Datasets Mentioned

BETA
PRJNA394021
PRJNA321963
PRJNA474413

Methods Mentioned

BETA
genotyping
amplicon
PCR
amplicon sequencing
Illumina sequencing

Software Mentioned

PrinSeq
Bowtie
SGE
Docker
SAMtools
SLURM
FastQC
GenomeDetective
Trimmomatic
SPAdes

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