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rMAP-docker Public
This Docker image provides a ready-to-use environment for rMAP, a bioinformatics pipeline for analyzing microbial genomic data & profiling AMR, Mobilome & Virulome. It includes all required tools &…
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ASFV-ONT-Gen Public
ASFV-ONT-Gen is a pipeline for analyzing African Swine Fever Virus (ASFV) whole-genome sequencing data generated using Oxford Nanopore Technology (ONT). It supports genome assembly & assembly stati…
phylogenetics variant-calling genome-assembly variant-annotation nanopore-sequencing african-swine-fever host-dna-removalPython MIT License UpdatedMay 22, 2025 -
gmboowa.github.io Public template
Forked from mikensubuga/mikensubuga.github.ioMy Personal Website: Publications, Repositories, Projects, Resources, Media
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pathogengenomics Public
Comprehensive genomic workflow - reference data retrieval, variant calling, custom database setup, annotation, & missense variant filtering
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nf-rMAP Public
nf-rMAP: Nextflow-powered microbial genomics pipeline for rapid antimicrobial resistance analysis. Implements rMAP's core functionality with cloud-native scalability, enhanced QC, & modular workflo…
Nextflow UpdatedMay 19, 2025 -
AMRSurveillanceDashboard Public
AMR Surveillance Dashboard is an interactive tool for visualizing AMR trends regionally. It provides dynamic insights into resistance patterns, genotypic markers, & lineage distribution across coun…
Python UpdatedMay 18, 2025 -
shared_variant_analyzer Public
This script analyzes variant call format (VCF) files to identify genetic variants shared across multiple samples. Given a list of VCF paths, it reports variants present in ≥10-100% of samples (10% …
Perl MIT License UpdatedMay 18, 2025 -
GenoSweep Public
GenoSweep is an automated genomic analysis pipeline processing raw FASTQs through quality control, host read removal, reference alignment (BWA), variant calling (bcftools), and consensus generation…
Shell UpdatedMay 16, 2025 -
extractonlymissenseSNPs Public
This script automates missense SNP extraction/counting from VCF files using BCFTools. Processes multiple samples, handles compressed formats, verifies dependencies, and generates standardized repor…
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annotate_variants.py Public
Annotate Variants with Gene Information from a GenBank Reference
Python MIT License UpdatedMay 16, 2025 -
This workflow processes human whole-genome sequencing data from raw FASTQs to annotated variants. It performs quality control (FastQC/MultiQC), BWA alignment, GATK-based variant calling with joint …
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Script summarizes Mycobacterium tuberculosis genotypes & drug resistance profiles from result files. It detects Uganda-specific lineages and resistance-associated mutations across key anti-TB drugs.
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This script performs bacterial genomic analysis - such as SNP calling & antibiotic resistance detection in Klebsiella pneumoniae (FastQC, Snippy, AMR gene screening)
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subsample_raw_fastq Public
This C script subsamples raw FASTQ files (single/paired-end). For paired-end, it synchronously selects read pairs from two files, ensuring retention of matched sequences. It reads input, randomly c…
C UpdatedMay 15, 2025 -
Bunya-ONT-Gen Public
Bunya-ONT-Gen is a modular pipeline for analyzing Bunyavirus genomes from Nanopore metagenomic data. It supports quality control, taxonomic classification, genome assembly, variant detection, and p…
Python MIT License UpdatedMay 14, 2025 -
TheiaProk-amr-visualizer Public
TheiaProk-amr-visualizer is a Python script for visualizing antimicrobial resistance (AMR) patterns globally using TSV outputs from Theiagen Public Health Bioinformatics workflows. It generates int…
Python UpdatedMay 7, 2025 -
extract_species_abundance.py Public
Script to extract species abundance from Kraken2 report file
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VaricellaGen Public
Forked from MicroBioGenoHub/VaricellaGenAn automated pipeline for genomic analysis of Varicella-zoster virus (VZV), including quality control, variant calling, consensus genome generation, and phylogenetics.
Shell UpdatedApr 2, 2025 -
pipeline-resources Public
Forked from pha4ge/pipeline-resourcesBioinformatics Pipeline and Visualization resources
Apache License 2.0 UpdatedOct 22, 2024 -
vcf-annotator Public
Forked from rpetit3/vcf-annotatorAdd biological annotations to variants in a given VCF file.
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HIV-DRIVES Public
Forked from MicroBioGenoHub/HIV-DRIVESShell GNU General Public License v3.0 UpdatedSep 27, 2023 -
https-alshedivat.github.io-al-folio- Public
Forked from yuminzhao91/yuminzhao91.github.ioThis is the repository for my personal website. I forked this repository from alshedivat / al-folio and modified the files. You can access my personal website through this link: https://yuminzhao91…
HTML MIT License UpdatedApr 5, 2023 -
rMAP Public
Forked from GunzIvan28/rMAPBacterial analysis toolbox for full ESKAPEE pathogen characterisation and profiling the resistome, mobilome, virulome & phylogenomics using WGS
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Kleborate Public
Forked from klebgenomics/KleboratePython GNU General Public License v3.0 UpdatedNov 30, 2018 -
MetaCompare Public
Forked from minoh0201/MetaCompareMetaCompare
Python MIT License UpdatedNov 16, 2018 -
snippy Public
Forked from tseemann/snippy✂️ ⚡ Rapid bacterial SNP calling and core genome alignments
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