An analysis and visualization platform for 'omics data
generating hardware accelerators for pangenomic graph queries
Pangenome graphs visualisation, distance computing, reconstruction of sequences and other utility functions
AMR/VF LGT focused bacterial genomics analysis workflow
Pangenome Analysis in Prokaryotes Lesson
Scripts and utilities for pangenomic/phylogenomic analysis of prokaryotic genomes. Scripts for the analysis of genomic features such as C-ARSC, N-ARSC, and intergenic spacer lengths are also included.
A nextflow pipeline to run the mummer pipelines (align genomes, call snps) and process outputs into sane formats.
Analysis of shared parts of a pangenome
Pangenomics Workshop Overview
Topological data analysis for Comparative Genomics
Library to parse, edit and handle in memory GFA graphs
This repo contains scripts used for the identification of phylogenetic marker genes (PMGs) in assembled metagenomic data. Code is provided for benchmarking this method on sequenced genomes as well as running this analysis on metagenomic data. These scripts are in development.
A sophisticated bioinformatics pipeline for bacterial pangenome analysis, integrating WGS and RNA-Seq data. It enhances genome completeness with hybrid assemblies, identifies core/accessory genes, and enables pangenome-level transcriptomic profiling. Built on Snakemake, it is scalable, customizable, and optimized for strain-specific insights.
A nextflow pipeline to run the mummer pipelines (align genomes, call snps) and process outputs into sane formats.
Introduction to Python: Pangenomics
Introduction to the Command Line for Pangenomics
CPANG19 - Computational PANGenomics (2019)
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