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Welcome to the GeneParliamentID wiki! This page offers a broad overview of the GeneParliamentID (GPID) pipeline.

Wiki contents

For details on the following topics, please visit the dedicated wiki pages:

• Setup
• Pipeline parameters
• Method calibration
• Interpretation
• Tutorial

Pipeline overview

The key steps of the GeneParliamentID pipeline are:

1. Select genes with performance of species identification above user-defined threshold
2. Align each gene against reference, select top match based on highest Bit-score
3. Remove low-confidence matches that don't meet the user-defined alignment filtering thresholds
4. Summarise all remaining identifications to the Gene Parliament
5. Flag the sample as data-deficient if the number of genes (parliament size) is below the user-defined threshold
6. Select identification with most support as the top identification
7. Evaluate confidence in the top identification based on the percentage of genes supporting this identification

For a worked example using test data, see the Tutorial.