A fully reproducible and state-of-the-art ancient DNA analysis pipeline
Genestrip - Efficient read classification, filtering and k-mer counting for selected groups of species
A collection of R functions to aid in host-pathogen genomic research
Create standalone HTML reports for tracking SNP clusters within NCBI Pathogen Detection
PathoLin is an automated, dynamic lineage assignment and nomenclature framework for viral pathogens based on haplotype network topology, with PathoLin-GRU for rapid lineage inference.
A selection of databases for Genestrip
Metagenomic pathogen-discovery workflow with host subtraction and competitive confirmatory mapping
Portable WDL/Cromwell workflow for microbial case-control GWAS from paired-end reads, producing annotated pyseer associations & HTML reports.
A comprehensive pan-immunophagomic analysis of Pseudomonas aeruginosa, characterizing CRISPR-Cas arrays, prophage integrations, and innate bacterial defense repertoires across diverse clinical isolates.
A Nextflow workflow to download standard datasets for public health
A genetic sequence analysis on calculating the GC contents and CpG deficiencies on multiple coronaviruses (SAR-CoV, SAR-CoV-2, MERS-CoV and 2 two bat derived SARS-like coronaviruses) to see which coronavirus has the most potentially effective mechanism to escape the anti-virus activities on human bodies.
Reproducible workflow powering the maintained Pakistan SARS-CoV-2 Nextstrain community build
Reproducible WPV1 phylogeographic analysis template with synthetic example data
Publication-linked RSV-A and RSV-B whole-genome analysis workflow for the Islamabad 2022–2023 study
Syed Adnan Haider — pathogen genomics, public-health bioinformatics and research notes
Publication-linked SARS-CoV-2 workflow for consensus generation, lineage assignment and phylogeny
Oxford Nanopore VP1 analysis pipeline for direct poliovirus detection, consensus calling and reporting
Academic personal website,
Publication-linked DENV-1 and DENV-2 workflow for consensus generation, phylogeny and mutation analysis
Publication-linked CCHFV workflow for segmented consensus, phylogeny and reassortment screening
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