Popular repositories Loading

1. rsv-islamabad-2022-2023-analysis rsv-islamabad-2022-2023-analysis Public

   Complete pipeline that mirrors the manuscript: reference based assembly with depth masking, de novo checks, phylogeny with configurable models including ModelFinder, and targeted mutation analysis …

   Python

2. cva24v-ahc-2023-analysis cva24v-ahc-2023-analysis Public

   End to end workflow for CV-A24v: trimming, de novo assembly, reference mapping with masked consensus, MAFFT alignment, IQ-TREE phylogenies for whole genome and VP1, and amino acid comparison agains…

   Python

3. ncov ncov Public

   Forked from NIH-BIGVI-PAKISTAN/ncov

   Genomic epidemiology of novel coronavirus (SARS-CoV-2) in Pakistan

4. denv-2023-pakistan-analysis denv-2023-pakistan-analysis Public

   End to end Snakemake workflow for DENV-1 and DENV-2. FastQC, Trimmomatic, Picard, SPAdes, BWA, bcftools masked consensus at depth 10, MAFFT, IQ-TREE with GTR+G+I, BLAST driven context fetching, pol…

   Python

5. mumps-2023-pakistan-analysis mumps-2023-pakistan-analysis Public

   End to end Snakemake workflow for MuV genotype G. FastQC, Trimmomatic, Picard, SPAdes, BWA, masked consensus at depth 10, MAFFT, IQ-TREE with K2+I for SH and GTR+G for whole genome. Includes SH ext…

   Python

6. polio-capsid-ngs-analysis polio-capsid-ngs-analysis Public

   Reproducible post-culture whole-capsid Illumina workflow for poliovirus. Reference-based consensus, antigenic site analysis across VP1-VP3, phylogeny, and optional de novo checks.

   Python