pangene for Mac

Getting Started

Getting Started Introduction Graph Construction Preparing a protein set Aligning proteins to genomes Constructing a pangene graph Analyzing a graph Graph Visualization Citation Limitations

Introduction

Pangene is a command-line tool to construct a pangenome gene graph. In this graph, a node repsents a marker gene and an edge between two genes indicates their genomic adjaceny on input genomes. Pangene takes the miniprot alignment between a protein set and multiple genomes and produces a graph in the GFA format. It attempts to reduce the redundancy in the input proteins and filter spurious alignments while preserving close but non-identical paralogs. The output graph can be visualized in generic GFA viewers such as BandageNG or via a web interface. Users can explore local human subgraphs at a public server. Prebuilt pangene graphs can be found at DOI:10.5281/zenodo.8118576.

Graph Construction

Pangene takes a list of protein-to-genome alignment as input. To generate these alignments, you need to align the same set of proteins to multiple genomes. How to choose the protein set can be tricky.

Preparing a protein set

For constructing a human pangene graph, the simplest choice is to use annotated genes in GRCh38. It is highly recommended to name a protein sequence like RGPD6:ENSP00000512633.1 where RGPD6 is the gene name and ENSP00000512633.1 is the unique protein identifier. In the output GFA, nodes are named after genes, so you would want to use human-readable gene names for visualization later. You may use the following command line to extract protein sequences from Ensembl or GenCode annotation:

With pangene, different isoforms or diverged alleles of the same gene can be present in the protein set, though in practice, we find selecting the canonical isoform per gene tends to give a cleaner graph probably possibly due to annotation errors among rare isoforms. For the GenCode annotation, use getaa -c to extract canonical isoforms only.

For a new species without good gene annotation, you may use protein annotations from a closely related species. You may pool proteins from multiple closely related species as well. Pangene aims to work with such input but this use case has not been thoroughly carefully evaluated. Given a bacteria pangenome of the same species, you may predict genes with existing tools, cluster them with CD-HIT or MMseqs2 and feed the representative protein in each cluster to pangene.

Aligning proteins to genomes

Pangene currently only works with miniprot's PAF output. We usually use the following command line:

For bacterial data, add -S to disable splicing.

Constructing a pangene graph

The following command-line constructs a pangene graph