Type: Article

Meeting the challenge of genomic analysis: a collaboratively developed workshop for pangenomics and topological data analysis

Haydeé Contreras-Peruyero; Shaday Guerrero-Flores; Claudia Zirión-Martínez; Paulina M Mejía-Ponce; Marisol Navarro-Miranda; J Abel Lovaco-Flores; José M Ibarra-Rodríguez; Anton Pashkov; Cuauhtémoc Licona-Cassani; Nelly Sélem-Mojica;

Abstract:

Motivation As genomics data analysis becomes increasingly intricate, researchers face the challenge of mastering various software tools. The rise of Pangenomics analysis, which examines the complete set of genes in a group of genomes, is particularly transformative in understanding genetic diversity. Our interdisciplinary team of biologists and mathematicians developed a short Pangenomics Workshop covering Bash, Python scripting, Pangenome, and Topological Data Analysis. These skills provide deeper insights into genetic variations and their implications in Evolutionary Biology. The workshop uses a Conda environment for reproducibility and accessibility. Developed in The Carpentries Incubator infrastructure, the workshop aims to equip researchers with essential skills for Pangenomics research. By emphasizing the role of a community of practice, this work underscores its significance in empowering multidisciplinary professionals to collaboratively develop training that adheres to best practices. Results Our workshop delivers tangible outcomes by enhancing the skill sets of Computational Biology professionals. Participants gain hands-on experience using real data from the first described pangenome. We share our paths toward creating an open-source, multidisciplinary, and public resource where learners can develop expertise in Pangenomic Analysis. This initiative goes beyond advancing individual capabilities, aligning with the broader mission of addressing educational needs in Computational Biology. Availability and implementation https://carpentries-incubator.github.io/pangenomics-workshop/