GitHub

Related Projects

Mycelia builds upon and complements several excellent projects in the graph genomics and bioinformatics space. This page acknowledges these tools and tracks their integration status with Mycelia.

Graph Genomics Tools

vg

The variation graph toolkit - a comprehensive suite for working with genome variation graphs. Mycelia wraps vg's core functionality for graph construction, manipulation, and analysis.

PGGB

PanGenome Graph Builder - a pipeline for constructing pangenome variation graphs from genome assemblies. Combines wfmash, seqwish, smoothxg, odgi, and gfaffix.

ODGI

Optimized Dynamic Genome/Graph Implementation - tools for analyzing and manipulating genome variation graphs. Provides graph optimization, visualization, and path analysis.

MetaGraph

A scalable framework for indexing and querying large-scale genomic databases using annotated de Bruijn graphs.

PanTools

Computational pan-genomics toolkit with a focus on database-driven pangenome analysis and comparative genomics.

pangene

Li Heng's tool for pangenome gene annotation - extracts and analyzes genes across multiple genomes in a pangenome context.

Graphein

Protein Graph Library - converts protein structures and interaction networks into graph representations for machine learning and network analysis.