Pan1c

Pan1c streamlines chromosome-level pangenome graph construction by generating pangenome graphs individually for each chromosome and concatenating them into a final graph, enabling parallelized construction and facilitating downstream analyses.

Key Features:

• Chromosome-by-chromosome construction: Pangenome graphs are generated individually for each chromosome and then concatenated into a final graph.
• Dual pangenome strategies: Integrates PGGB and Minigraph-Cactus as complementary pangenome construction methods.
• Parallelization: Reduces construction time through parallelized chromosome-level graph generation.
• Quality assessment outputs: Produces various graphs and statistics for pangenome graph quality evaluation and interpretation.
• Visualization integration: Results are accessible via a web page generated by Pan1c-view.

Scientific Applications:

• Assembly validation: Benchmarking on human, fungal, and wheat assemblies demonstrates utility for assembly and graph validation across diverse genome sizes and complexities.
• Graph validation: Enables assessment of pangenome graph quality through informative metric plots and graphics.
• Primary pangenome analysis: Supports initial downstream analyses of genomic variation represented in graph references.
• Variant calling improvement: Facilitates inclusion of all genomic variations in graph references to improve sequence alignment rate, quality, and variant calling accuracy.

Methodology:

Pan1c is implemented as a Snakemake workflow that employs a chromosome-by-chromosome graph construction strategy, integrating PGGB or Minigraph-Cactus for pangenome generation and producing metric plots and graphics using a large set of tools.