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