This repository contains the steps used for analyzing Whole Genome Sequencing (WGS) and Targeted Genome Sequencing (TGS) data of Dengue Virus serotype 3 (DENV3) isolates from the Kenyan Coast in 2019. The research explores the genetic characteristics and transmission dynamics of DENV3 in this region.
- trimmomatic - http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf
- trim-galore - https://github.com/FelixKrueger/TrimGalore
- fastqc - https://github.com/golharam/FastQC
- bwa - http://bio-bwa.sourceforge.net/bwa.shtml
- Cutadapt - https://github.com/marcelm/cutadapt
- samtools - http://www.htslib.org/doc/samtools.html
- ivar - https://github.com/andersen-lab/ivar#readme
- NGS-mapper- https://github.com/VDBWRAIR/ngs_mapper
- jmodeltest: https://github.com/ddarriba/jmodeltest2
- phyml: https://github.com/stephaneguindon/phyml
- iqtree: http://www.iqtree.org/
- beast-mcmc: https://github.com/beast-dev/beast-mcmc
- figtree: https://github.com/rambaut/figtree/releases/tag/v1.4.4
- mafft <- good for very large alignments
- muscle <-fast good for midsized alignments
- CLC genomic workbench
- https://www.bv-brc.org/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10021577/
- Kimita Gathii
- Feel free to explore the provided tools and methodology for your own research or to gain insights into our DENV3 analysis.