PGR-TK: Pangenome Research Tool Kit

Long-read aligner to pangenome graphs

Pairing reads on genome graphs

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

An accurate GFF3/GTF lift over pipeline

Bifrost graph gene caller.

keep track of some scripts used to evaluate rgfa stuff

Tool for parsing and converting between alternate representations of phased assemblies in GFA format

Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation

Remove human reads from a sequencing run

geNomad: Identification of mobile genetic elements

Gfapy: a flexible and extensible software library for handling sequence graphs in Python

↙️ ↘️ An R package for working with causal directed acyclic graphs (DAGs)

implicit pangenome graph

Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index

Statistics and analysis for variation graphs

Library containing useful building blocks for bioinformatics software

Application of pan-genome for population

Kun-peng: an ultra-fast, low-memory footprint and accurate taxonomy classifier for all

Mumemto: multi-MUM and MEM finding across pangenomes