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Abstract

To study microorganisms present in an environment, many tools are needed. Each of these tools generates a large number of results files, providing different insights. PANKEGG is an all-in-one tool that centralises these results files and helps researchers navigate and visualise them for comparison, interpretation, and understanding of microbial communities in the environment. PANKEGG supports researchers by parsing and visualising metagenome-assembled genomes (MAGs) and exploring their metabolic capabilities. It integrates quality metrics, annotation, and taxonomic classification in one interactive central database. PANKEGG enables researchers to explore, compare, and interpret their data through a modern browser-based interface, streamlining the analysis of large and complex metagenomic datasets. The software supports output from widely used tools such as CheckM2 (Chklovski et al., 2022), GTDB-TK (Chaumeil et al., 2020), Sourmash (Brown & Irber, 2016), and EggNOG (Cantalapiedra et al., 2021), making it a flexible solution for a wide range of microbiome and environmental genomics studies. By interconnecting the different analysis results, researchers can investigate different interactions in the data more visually and conveniently. PANKEGG answers questions such as: • How many of my bins pass the GTDB (Parks et al., 2022) quality threshold? • What is their taxonomic classification? • Which Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologs are present? • Which proportion of their respective metabolic pathways is covered by the KEGG orthologs identified? Answering these questions typically requires inspecting multiple result files and cross-referencing the information. In contrast, PANKEGG provides an all-in-one platform to explore, visualise, interpret, and save the results.

Published in

Journal of open source software
2025, volume: 10, number: 116, article number: 9188

SLU Authors

UKÄ Subject classification

Microbiology

Publication identifier

  • DOI: https://doi.org/10.21105/joss.09188

Permanent link to this page (URI)

https://res.slu.se/id/publ/145356