MetaPathways v3.5: Modularity and Scalability Improvements for Pathway Inference from Environmental Genomes

Abstract

AbstractOver the past decade MetaPathwayshas advanced as a modular pipeline for constructing environmental pathway genome databases (ePGDBs), increasing our understanding of microbial metabolism at the individual, population and community levels of biological organization. With this release, we have addressed several user experience issues related to installation, module integration, and database management. With a refactored code base, MetaPathwaysv3.5 enhances the user experience through streamlined installation via package indexes or containers, refined modules, and interface upgrades. It boasts updated algorithm support for sequence feature prediction, annotation, metabolic inference, and coverage metrics including genome resolved metagenomes. Tested and refined on synthetic datasets, MetaPathwaysv3.5 demonstrates improved performance and usability; facilitating more in-depth exploration of microbial interactions and metabolic functions in environmental genomes that scales with con-temporary sequencing throughput.Availability and ImplementationMetaPathwaysv3.5 is availableviaAnaconda, Docker, and Apptainer. The source code is available on BitBucket:https://bitbucket.org/BCB2/metapathways/The documentation is available via ReadTheDocs:https://metapathways.readthedocs.ioContactshallam@mail.ubc.ca