Panacus: fast and exact pangenome growth and core size estimation.

ABSTRACT:

Motivation

Using a single linear reference genome poses a limitation to exploring the full genomic diversity of a species. The release of a draft human pangenome underscores the increasing relevance of pangenomics to overcome these limitations. Pangenomes are commonly represented as graphs, which can represent billions of base pairs of sequence. Presently, there is a lack of scalable software able to perform key tasks on pangenomes, such as quantifying universally shared sequence across genomes (the core genome) and measuring the extent of genomic variability as a function of sample size (pangenome growth).

Results

We introduce Panacus (pangenome-abacus), a tool designed to rapidly perform these tasks and visualize the results in interactive plots. Panacus can process GFA fi

SUBMITTER: Parmigiani L 

PROVIDER: S-EPMC11665632 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature