CIEVAD

CIEVAD comprises Nextflow workflows that facilitate end-to-end testing of genomic variant detection through synthetic test data generation and evaluation of variant sets against that data.

Key Features:

• Synthetic Test Data Generation: Workflows generate synthetic test data for benchmarking genomic variant detection methods.
• Variant Set Evaluation: Workflows evaluate the accordance of user-provided variant sets against the generated test data.
• Modifiable Architecture: The workflows are highly modifiable to accommodate diverse testing scenarios.
• Nextflow Implementation: All workflows are implemented in Nextflow for portable and reproducible execution.

Scientific Applications:

• Small Genomic Variant Detection Validation: CIEVAD validates detection of single or few nucleotide variants where precise genomic location and nucleotide change identification is critical for phenotype analysis.
• Benchmarking Variant Calling Pipelines: CIEVAD enables systematic comparison and quality assessment of methods across the variant detection workflow.

Methodology:

The workflows are implemented in Nextflow and operate through two main components: generation of synthetic test data and evaluation of variant set accordance with that data.