A fully reproducible and state-of-the-art ancient DNA analysis pipeline

A collection of R functions to aid in host-pathogen genomic research

Genestrip - Efficient read classification, filtering and k-mer counting for selected groups of species

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.

Panel driven metagenomic confirmatory mapping pipeline with host subtraction and competitive mapping for bacteria, viruses, fungi, and parasites

A selection of databases for Genestrip

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 for RSV-A and RSV-B whole genome analysis that mirrors the Islamabad 2022 to 2023 study.

Reproducible WPV1 phylogeographic analysis template with synthetic example data

End to end Snakemake workflow for iSeq amplicon data. FastQC, Trimmomatic, BWA, SAMtools and bcftools consensus at depth 10, Pangolin lineage assignment, MAFFT alignment, IQ-TREE with ultrafast bootstraps and optional ModelFinder, optional Augur plus TreeTime for time-resolved trees, and utilities to fetch context genomes from GenBank.

Academic personal website,

Syed Adnan Haider pathogen genomics blog

Standalone ONT MinION VP1 analysis pipeline for DDNS stool-culture amplicon sequencing

Reproducible Pakistan SARS-CoV-2 Nextstrain build workflow

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 extraction, HN and F mutation tables, BLAST based context fetching, and full references with citation.

Reproducible Snakemake pipeline for CCHFV: SPAdes contigs, BLAST driven clade selection per segment, BWA mapping with masked consensus for S, M, and L, MAFFT plus IQ-TREE phylogeny, and reassortment flagging.

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, polyprotein translation and mutation tables. Includes full references and citation.

GitHub profile README for Syed Adnan Haider