This App allows the user to view summaries of the Genomes in a Genome Set. This includes any taxonomic classification, tallies of feature types (e.g. number of protein encoding genes, ribosomal RNA genes, etc.). Optionally, and slower, the user can include quality completeness and contamination measures from CheckM, and environmental bioelement processing functional summaries.

Tool and Data Sources:

MicroTrait v1.0 HMMs are installed from https://github.com/ukaraoz/microtrait-hmm/tree/master/data.kb_hmmer/hmm

CheckM v1.1.2 is installed from https://github.com/Ecogenomics/CheckM/releases/tag/v1.1.2 with reference data version 2015_01_16 from https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz.

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
• Karaoz U, Brodie EL. microTrait: A Toolset for a Trait-Based Representation of Microbial Genomes. Front Bioinform. 2022 Jul 22;2:918853. doi: 10.3389/fbinf.2022.918853
• Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25: 1043 1055. doi:10.1101/gr.186072.114