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Welcome to the GeneParliamentID wiki!

This page provides links to the wiki contents and provides an overview of the GeneParliamentID (GPID) pipeline.

Wiki contents

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

• Setup
• Pipeline parameters
• Interpretation
• Method calibration
• 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 the number of genes supporting each identification 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.