GAMBIT_Query¶
Quick Facts¶
| Workflow Type | Applicable Kingdom | Last Known Changes | Command-line Compatibility | Workflow Level |
|---|---|---|---|---|
| Standalone | Bacteria, Mycotics | PHB v2.2.0 | Yes | Sample-level |
GAMBIT_Query_PHB¶
The GAMBIT_Query_PHB workflow performs taxon assignment of a genome assembly using the GAMBIT task.
Inputs¶
| Terra Task Name | Variable | Type | Description | Default Value | Terra Status |
|---|---|---|---|---|---|
| gambit_query | assembly_fasta | File | Assembly file in FASTA format | Required | |
| gambit_query | samplename | String | Sample name | Required | |
| gambit | cpu | Int | Number of CPUs to allocate to the task | 8 | Optional |
| gambit | disk_size | Int | Amount of storage (in GB) to allocate to the task | 100 | Optional |
| gambit | memory | Int | Amount of memory/RAM (in GB) to allocate to the task | 16 | Optional |
| gambit | docker | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/staphb/gambit:1.0.0" | Optional |
| gambit | gambit_db_genomes | File | Database of metadata for assembled query genomes; requires complementary signatures file. If not provided, uses default database "/gambit-db" | "gs://gambit-databases-rp/2.0.0/gambit-metadata-2.0.0-20240628.gdb" | Optional |
| gambit | gambit_db_signatures | File | Signatures file; requires complementary genomes file. If not specified, the file from the docker container will be used. | "gs://gambit-databases-rp/2.0.0/gambit-signatures-2.0.0-20240628.gs" | Optional |
Workflow Tasks¶
GAMBIT determines the taxon of the genome assembly using a k-mer based approach to match the assembly sequence to the closest complete genome in a database, thereby predicting its identity. Sometimes, GAMBIT can confidently designate the organism to the species level. Other times, it is more conservative and assigns it to a higher taxonomic rank.
For additional details regarding the GAMBIT tool and a list of available GAMBIT databases for analysis, please consult the GAMBIT tool documentation.
GAMBIT Technical Details
| Links | |
|---|---|
| Task | task_gambit.wdl |
| Software Source Code | GAMBIT on GitHub |
| Software Documentation | GAMBIT ReadTheDocs |
| Original Publication(s) | GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking): A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification |
Outputs¶
| Variable | Type | Description |
|---|---|---|
| gambit_closest_genomes | File | CSV file listing genomes in the GAMBIT database that are most similar to the query assembly |
| gambit_db_version | String | Version of the GAMBIT database used |
| gambit_docker | String | GAMBIT Docker used |
| gambit_predicted_taxon | String | Taxon predicted by GAMBIT |
| gambit_predicted_taxon_rank | String | Taxon rank of GAMBIT taxon prediction |
| gambit_query_wf_analysis_date | String | Date of analysis |
| gambit_query_wf_version | String | PHB repository version |
| gambit_report | File | GAMBIT report in a machine-readable format |
| gambit_version | String | Version of gambit software used |
GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking): A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification. Lumpe et al. PLOS ONE, 2022. DOI: 10.1371/journal.pone.0277575