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.
Show 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 strategies 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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