Allows user to create a GenomeSet without specifying names
This App allows the user to group individual Genome objects into a Genome Set.
Description
Batch Create Genome Set allows a user to create a Set of Genomes which can be used in subsequent Apps that operate on Genome Sets. Each Genome object must already be within the Narrative's data workspace, so if there are genomes from other Narratives or genomes from the public reference genome library that the user wishes to include, they must first be imported into the active Narrative. All Genomes that match the Name Pattern will be included in the Set. If the Name Pattern is left blank, all genome objects in the current Narrative will be included.Example allowed Name Patterns:
- *.Genome
- Sample_1-*
- Sample_1-*.Genome
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_Batch_Create_GenomeSetModule Commit: 79b273010c6c30b9343e03b64b7d7502ded704ce