Supplementary Material/Data for "DEN-IM: Dengue virus genotyping from amplicon and shotgun metagenomic sequencing" as published in Microbial Genomics

Supplementary Material/Data for "DEN-IM: Dengue virus genotyping from amplicon and shotgun metagenomic sequencing" as published in Microbial Genomics

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. 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 4 CHIKV, 16 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.

Supplemental material for the manuscript "DEN-IM: Dengue virus genotyping from shotgun and targeted metagenomics".

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 samplesThe 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.

Supplemental material for the manuscript "DEN-IM: Dengue virus genotyping from shotgun and targeted metagenomics".

Supplemental material for the manuscript "DEN-IM: Dengue virus genotyping from shotgun and targeted metagenomics".

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 samplesThe 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.

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. 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 analyses were executed with the default resources and parameters, with the option to include the closest typing reference in the final tree set to true on the shotgun metagenomics dataset. The resulting HTML reports for both analysis are available as compressed files.

We have compiled a database of 3830 complete DENV genomes obtained from the NIAID Virus Pathogen Database and Analysis Resource (ViPR) in January 2019 (1) (http://www.viprbrc.org/). A representative of DENV serotype 1 genotype III was introduced (EF457905, recovered from monkey) as no representatives were available with the search criteria used.Overly similar sequences in the collection were removed from the database by clustering the sequences in each serotype at 98% nucleotide similarity, leaving 161 representative sequences of all described DENV serotypes and genotypes, with 46 DENV-1 sequences, 63 DENV-2 , 25 DENV-3 and 27 DENV-4.
Phylogenetic analysis of typing collection was performed by aligning the full reference genomes with MAFFT, in auto mode and with automatic sequence orientation adjustment. A phylogenetic tree was inferred with RAxML (version 8.12.11) using the GTR-𝛤 substitution model and 500 times bootstrap. Additionally, the same analysis was performed with the envelope protein (E) only. The resulting trees are available here.