Allows users to extract a GenomeSet from a FeatureSet.
Build Genome Set from Feature Set allows a user to extract Genomes from a FeatureSet and make a GenomeSet object from them. The features themselves in a FeatureSet object contain the information about which genomes they are associated with, so this information is extracted to form the output GenomeSet.
Note: Features from Annotated Metagenome Assembly objects are skipped so that output GenomeSet only contains Genome Objects.
Team members who developed & deployed App in KBase: Dylan Chivian. For questions, please contact us.
Please cite:
- Chivian D, Jungbluth SP, Dehal PS, Wood-Charlson EM, Canon RS, Allen BH, Clark MM, Gu T, Land ML, Price GA, Riehl WJ, Sneddon MW, Sutormin R, Zhang Q, Cottingham RW, Henry CS, Arkin AP. Metagenome-assembled genome extraction and analysis from microbiomes using KBase. Nat Protoc. 2023 Jan;18(1):208-238. doi: 10.1038/s41596-022-00747-x
Related Publications
- Chivian D, Jungbluth SP, Dehal PS, Wood-Charlson EM, Canon RS, Allen BH, Clark MM, Gu T, Land ML, Price GA, Riehl WJ, Sneddon MW, Sutormin R, Zhang Q, Cottingham RW, Henry CS, Arkin AP. Metagenome-assembled genome extraction and analysis from microbiomes using KBase. Nat Protoc. 2023 Jan;18(1):208-238. doi: 10.1038/s41596-022-00747-x , https://www.nature.com/articles/s41596-022-00747-x
- Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology. 2018;36: 566. doi: 10.1038/nbt.4163 , https://www.nature.com/articles/nbt.4163
App Specification:
https://github.com/kbaseapps/kb_SetUtilities/tree/79b273010c6c30b9343e03b64b7d7502ded704ce/ui/narrative/methods/KButil_Build_GenomeSet_from_FeatureSetModule Commit: 79b273010c6c30b9343e03b64b7d7502ded704ce