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bioRxiv · 10.64898/2026.04.17.719212

Pan1c : a pipeline to easily build chromosome-level pangenome graphs

Mergez, A.·Racoupeau, M.·Bardou, P.·Linard, B.·Legeai, F.·Choulet, F.·Gaspin, C.·Klopp, C.
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Abstract

The advances of sequencing technologies and the availability of high-quality genome assemblies for many genotypes per species, give the opportunity to improve sequence alignment rate and quality, and the variant calling accuracy by including all genomic variations in a graph reference, called a pangenome graph. Because the process of building and analysing a pangenome graph is still complex, with related software packages under development, there is an important need for releasing user-friendly pipelines for this emerging research area. Pan1C is a pipeline based on a chromosome-by-chromosome graph construction strategy. It integrates two complementary strate-gies for building pangenomes and produces informative metric plots and graphics using a large set of tools. By benchmarking Pan1C on human, fungal, and wheat assemblies, which span a wide range of genome sizes and complexities, we showed the interest of Pan1C for assembly and graph validation as well as for performing primary analyses.

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Mergez, A., Racoupeau, M., Bardou, P., Linard, B., Legeai, F., Choulet, F., Gaspin, C., Klopp, C.. 2026-04-21. Pan1c : a pipeline to easily build chromosome-level pangenome graphs. https://doi.org/10.64898/2026.04.17.719212

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