DEN-IM: Dengue virus genotyping from amplicon and shotgun metagenomics - HTML reports

To evaluate the DEN-IM’s workflow performance, we analysed two datasets, one containing shotgun metagenomics sequencing data of patient samples, and a second with targeted metagenomics sequencing data obtained from PRJNA394021 ( 106 paired-end samples) and PRJNA321963 (78 single-end samples).
The shotgun metagenomic dataset comprised of 22 shotgun metagenomics paired-end short-read Illumina sequencing samples datasets from clinical positive dengue cases (identified as such by a positive qRT-PCR/RT-PCR test and seroconversion test), one positive control (purified from a DENV culture), one negative control (blank), and an in vitro spiked sample containing the 4 DENV serotypes.
The third dataset contains publicly available sequences, both from shotgun and targeted metagenomics, containing 45 CHIKV, 66 ZKV, and 21 YFV samples
The analyses were executed with the default resources and parameters, with the option to include NCBI references and the closest typing reference in the final tree set to true on the shotgun metagenomics dataset. The resulting HTML reports for all analysis are available as compressed files. To open the report in your default browser uncompress the folders and open the pipeline_report.html file inside.