MetaPathways v2.5
Kishori M. Konwar, Niels W. Hanson, Maya P. Bhatia, Dongjae Kim, Shang-Ju Wu, Aria S. Hahn, Connor Morgan-Lang, Hiu Kan Cheung, and Steven J. Hallam
Abstract
The rise of next-generation sequencing technologies is producing vast amounts of sequence information from natural and engineered ecosystems. While this environmental information has the potential to transform our modern worldview and drive biotechnological innovation knowledge creation and translation is limited by the availability of adaptive software tools that scale with increasing data processing, management and analytic requirements. Here we present improvements to MetaPathways a modular annotation and analysis pipeline that identify pathway prediction hazards through integration of a weighted taxonomic distance and enable quantitative comparison of de novo assembled environmental sequence information through a normalized read-mapping measure. Additionally we improve implementation of LAST homology searches through BLAST-equivalent E-values and output format enabling natively compatible functional annotations with prevailing software applications. Finally, an updated MetaPathways GUI allows for keyword annotation query and projection onto user defined functional gene hierarchies including the Carbohydrate-Active Enzyme (CAZy) database.
Downloads for this Release:
- metapathways2-2.5.zip (link below): Python source code folder
metapathways2-2.5 - MetaPathways_DBs.zip: Database folder with required reference files (new CAZy hierarchy included)
- CAZY_2014_09_04.zip: CAZy sequences with custom annotation formatting for MetaPathways v2.5
More installation information can be found on the wiki.