Build a partitioned pangenome graph from microbial genomes

Constructing a pangenome gene graph

GET_HOMOLOGUES: a versatile software package for pan-genome analysis

A bioinformatic toolkit to align genome assemblies into pangenome graphs

Panacus is a tool for computing statistics for GFA-formatted pangenome graphs

Renders a collection of sequences into a pangenome graph. https://doi.org/10.1093/bioinformatics/btae609.

Panache is a web-based interface designed for the visualization of linearized pangenomes. It can be used to show presence/absence information of pangenomic blocks of sequence or genes in a browser-like display.

PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples

Long read aligner for cyclic and acyclic pangenome graphs

Integrate multiple genome assemblies into a pangenome graph

Pangenome graphs visualisation, distance computing, reconstruction of sequences and other utility functions

A comprehensive and intuitive encapsulated OO class system for analyzing bacterial pangenomes in R.

Workflow to construct linear representation of pan genome from deep WGS data and public assemblies

Strain-level abundances estimation in metagenomic samples using variation graphs

Practical Haplotype Graph (PHG) version 2

Structure variants calling and genotyping scripts for pan-Zea

Pangenome analysis of eukaryotes.

the miscellaneous analysis scripts used in the research of pan-Zea genome and genetics

A toolkit for quality control & adjustment of nucleotide redundancy in bacterial pan-genome analyses

Non-redundant pangenome assemblies from multiple genomes or bins