AI Article Synopsis
- - Using only one linear reference genome limits the understanding of genomic diversity; the draft human pangenome shows the need for pangenomics to address these gaps and capture more genetic variation.
- - A new tool called Panacus (pangenome-abacus) has been developed to efficiently analyze pangenomes, capable of processing large human pangenome graphs quickly, producing interactive visualizations in under an hour.
- - Panacus is open-source and built in Rust, available for installation through Bioconda, with its source code and documentation accessible on GitHub.
Article 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 files, the accepted standard for pangenome graphs, and is able to analyze a human pangenome graph with 110 million nodes in <1 h.
Availability And Implementation: Panacus is implemented in Rust and is published as Open Source software under the MIT license. The source code and documentation are available at https://github.com/marschall-lab/panacus. Panacus can be installed via Bioconda at https://bioconda.github.io/recipes/panacus/README.html.
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11665632 | PMC |
| http://dx.doi.org/10.1093/bioinformatics/btae720 | DOI Listing |
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