Evidence of dengue virus transmission and a diverse Aedes mosquito virome on the Democratic Republic of Congo-Angola border_bash scripts

The code in this project accompanies an effort to investigate the virome of wild-caught Aedes mosquitoes from Kimpese, the Democratic Republic of the Congo (DRC). The DRC is the second largest country in Africa and has an estimated population of over 100 million. Its tropical climate is conducive to mosquito survival. Considerable attention is devoted to the high burden of malaria in the DRC, but arboviruses remain neglected, with limited studies of humans and mosquitoes to-date. To improve our understanding of the role of Aedes mosquito vectors in arboviral transmission in the DRC, we collected and sequenced the virome of mosquito pools from three areas of Kimpese, a region near the Angola border which has experienced recent arboviral outbreaks. Full details of this project can be found within this pre-print: Evidence of dengue virus transmission and a diverse Aedes mosquito virome on the Democratic Republic of Congo-Angola border (DOI: Evidence of dengue virus tr…). Details of the code are available at: github.com Overview of the scripts found here: a. Metagenomic analysis.sh # Bash script for metagenomic data analysis to explore virome in Aedes mosquitoes in the DRC. This file contains the needed code for paired-end reads merging, adaptor removal, reads filtering, taxonomic classification, and phylogenetic analysis. 1. Due to the storage limitations of Code Ocean, the sample dataset provided is a subset of our larger sequencing dataset. The full sequencing dataset is available at NCBI SRA, BioProject ID PRJNA1200724. To run the full dataset, please download it to your local computer or computer cluster. 2. Due to storage limitations, we use four sequences to build a small custom database for taxonomic classification in Code Ocean. As a result, all reads in the report files will be unclassified. To process the entire dataset, please use the default KrakenUniq nt and viral databases. 3. Due to Code Ocean resource limitations, only a subset of published/reference FASTA files from our final analysis are included in this capsule. Inclusion of all FASTAs during phylogenetic analysis results in significant increases in run time. All files are available through the Github link above. b. Nanopore targeted sequencing analysis.sh #Bash script for nanopore data analysis to explore mosquito species and blood meal. This file contains the needed code for basecalling, quality-filtering, and blast analysis. The sequencing dataset is available at NCBI SRA, BioProject ID PRJNA1200731. 1. Due to storage limitations in Code Ocean, we are unable to download the nt database, and it is not pre-installed. Running the blast command in Code Ocean will result in empty TXT files and a BLAST database error message. To obtain results, please download the nt database to your local computer or computer cluster. *Bash scripts rely on functioning installations of BBMerge (version 38.96), Trimmomatic (version 0.36), bwa-mem2 (version 2.2.1), SAMtools (version 1.21), SPAdes (version 4.0.0), KrakenUniq (version 1.0.4), Guppy (version 6.5.7), Blast (version 2.14.1), IQ-TREE (version2.4.0), and RAxML-NG. Installing all tools could take 1–1.5 hours. Use package managers (e.g., conda, brew, or apt) for faster installations. *These scripts can be run on the sequencing data available at NCBI SRA, BioProject IDs PRJNA1200724 and PRJNA1200731. To run the entire dataset, please download the datasets and required databases to your local computer or computer clusters. Running of the "metagenomic data analysis.sh" usually takes days to weeks but may vary depending on access to computer cluster resources and use of the SLURM system. Due to large size of the publicly available dataset, analysis may not be feasible on a conventional desktop computer without substantial memory enhancements. Running of the "Nanopore targeted sequencing analysis.sh" usually takes less than 2 days when appropriate computing cluster resources and the SLURM system are utilized.