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 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.

为评估DEN-IM的工作流性能，本研究共分析了两类数据集：其一包含患者样本的鸟枪宏基因组测序（shotgun metagenomics sequencing）数据，其二为取自生物项目编号PRJNA394021（含106对双端样本）与PRJNA321963（含78个单端样本）的靶向宏基因组测序（targeted metagenomics sequencing）数据。该鸟枪宏基因组数据集包含22份来自临床确诊登革热病例（经qRT-PCR/RT-PCR阳性检测及血清转换试验确认）的伊卢米纳（Illumina）双端短读长测序样本、1份登革病毒（Dengue Virus, DENV）培养纯化阳性对照、1份空白阴性对照，以及1份包含4种登革病毒血清型的体外加标样本。另有第三类数据集包含公开可用的宏基因组序列，涵盖鸟枪宏基因组与靶向宏基因组两类，包含45份基孔肯雅病毒（Chikungunya Virus, CHIKV）样本、66份ZKV样本及21份黄热病毒（Yellow Fever Virus, YFV）样本。
所有分析均采用默认资源与参数执行，在该鸟枪宏基因组数据集的分析中，将"纳入美国国家生物技术信息中心（National Center for Biotechnology Information, NCBI）参考序列"及"在最终系统发育树中纳入最相近分型参考序列"的选项均设置为真。所有分析生成的HTML报告均以压缩文件形式提供。如需在默认浏览器中打开报告，请先解压对应文件夹，再打开其中的pipeline_report.html文件。