Summary: Next-generation sequencing is producing vast amounts of sequence information from natural and engineered ecosystems. While this data deluge has enormous potential to transform our lives, knowledge creation and translation need software applications that scale with increasing data processing and analysis requirements. Here, we present improvements to MetaPathways, an annotation and analysis pipeline for environmental sequence information that expedites this transformation. We specifically address pathway prediction hazards through integration of a weighted taxonomic distance and enable quantitative comparison of assembled annotations through a normalized read-mapping measure. Additionally, we improve LAST homology searches through BLAST-equivalent E-values and output formats that are natively compatible with prevailing software applications. Finally, an updated GUI allows for keyword annotation query and projection onto user defined functional gene hierarchies, including the Carbohydrate-Active Enzyme database.

Availability and Implementation: MetaPathways v2.5 is available on GitHub: http://github.com/hallamlab/metapathways2

Contact: shallam@mail.ubc.ca

Supplementary information: Supplementary data are available at Bioinformatics online.