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Welcome to the GeneParliamentID wiki! This page offers a broad overview of the GeneParliamentID (GPID) pipeline.
For details on the following topics, please visit the dedicated wiki pages:
- A set of multipe genes for a sample of unknown identity
- A reference data set containing the same genes for the lineage of interest
- Calibration files to set pipeline parameters
- Optional: Classification file that specifies user-defined groups of closely related species
For detailed instructions, see Pipeline parameters.
- Select genes with performance of species identification above user-defined threshold
- Align each gene against reference, select top match based on highest Bit-score
- Remove low-confidence matches that don't meet the user-defined alignment filtering thresholds
- Summarise all remaining identifications to the Gene Parliament
- Flag the sample as data-deficient if the number of genes (parliament size) is below the user-defined threshold
- Select identification with most support as the top identification
- Evaluate confidence in the top identification based on the percentage of genes supporting this identification
The pipeline produces three output files:
- Table of Gene Parliament
- Visualisation of Gene Parliament
- Table of top identification
For interpretation of these outputs, see Interpretation of results.
Example outputs of identification of a mahogany timber sample are given below.
File <Sample1>_gpid.csv:
| Rank | Identification | Species Group | Support (%) | Support (count) |
|---|---|---|---|---|
| 1 | Entandrophragma angolense | Entandrophragma | 75.82 | 138 |
| 2 | Entandrophragma excelsum | Entandrophragma | 16.48 | 30 |
| 3 | Entandrophragma delevoyi | Entandrophragma | 3.85 | 7 |
| 4 | Entandrophragma congoense | Entandrophragma | 2.75 | 5 |
| 5 | Khaya ivorensis | Khaya | 0.55 | 1 |
| 5 | Swietenia humilis | Swietenia | 0.55 | 1 |
File <Sample1>_gpid.pdf:
The top identification is the species supported by the largest proportion of genes in the Gene Parliament. The table includes a data check and confidence estimate. The data check is a test whether the user-definied minimum parliament size is met. The confidence estimate is based on the support for the top identification and method calibration using a set of test samples.
- Probability correct: correct identification to species
- Probability close: correct identification to user-defined species group
- Probability wrong: incorrect identification
File <Sample1>_topid.csv:
| Rank | Identification | Species Group | Support (%) | Support (count) | Parliament size (count) | Data check | Probabilty correct (%) | Probability close (%) | Probability wrong (%) |
|---|---|---|---|---|---|---|---|---|---|
| 1 | Entandrophragma angolense | Entandrophragma | 75.82 | 138 | 182 | PASS | 100 | 0 | 0 |
To identify the optimal pipeline parameters for a given lineage, we strongly recommend conducting method calibration using the provided script. Method calibration also requires a set of test samples of known identity. The calibration script helps you to select the optimal parameters that balance accuracy of identification against retrievability of samples.
Method calibration includes the following steps:
- Select the optimal alignment filtering thresholds
- Calculate gene performance (percentage of correct identifications) following application of optimal alignment filters
- Select optimal gene performance threshold
- Select minimum parliament size threshold
- Estimate confidence of identification depending on the percentage of genes supporting the top identification