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

strange cross-platform, performance-oriented and interactive pangenome and large graph visualization

Long read aligner for cyclic and acyclic pangenome graphs

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

Integrate multiple genome assemblies into a pangenome graph

Practical Haplotype Graph (PHG) version 2

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

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

Strain-level abundances estimation in metagenomic samples using variation graphs

PanTE: A Comprehensive Framework for Transposable Element Discovery in Graph-based Pangenomes

Structure variants calling and genotyping scripts for pan-Zea

Pangenome analysis of eukaryotes.

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

Embedding-based indexing for compact storage and rapid querying of bacterial pan-genomes

Pangenome-based structural variation caller

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

A Nextflow pipeline for genome and pan-genome annotation

AlfaPang builds pangenome graphs without alignments or references.

Non-redundant pangenome assemblies from multiple genomes or bins

Compares pangenome graphs by calculating the segmentation distance between two GFA (Graphical Fragment Assembly) files.

Flexible workflow designed for bacterial WGS analyses (annotation, core/pan-genome reconstruction, phylogeny)

Pangenome structural variation (SV) merging and deduplication

luigi based workflow for analysising WGS samples collecting from different source. It will auto clustering, annotating gene or species, and finally perform pangenome analysis(roary).