Halvade

Halvade parallelizes post-sequencing DNA analysis by executing read mapping and variant calling pipelines across multi-node and multi-core compute infrastructures to accelerate whole-genome and whole-exome sequencing analyses.

Key Features:

• Pipeline steps: Executes read mapping followed by variant calling.
• GATK Best Practices compliance: Implements a DNA sequencing analysis pipeline that adheres to the Genome Analysis Toolkit (GATK) Best Practices recommendations.
• Supported sequencing types: Supports whole genome and whole exome sequencing.
• Parallel execution: Enables parallel execution of sequencing pipelines across multi-node and multi-core compute infrastructures.
• High parallel efficiency: Demonstrated processing of the NA12878 dataset (human, 100 bp paired-end reads, 50× coverage) in less than three hours on a 15-node cluster with 360 CPU cores.
• Single-machine acceleration: Provides substantial speedup on single multi-core machines compared to multithreading of individual tools.

Scientific Applications:

• Whole-genome sequencing (WGS): Accelerates read mapping and variant calling for WGS datasets, including high-coverage human genomes such as NA12878.
• Whole-exome sequencing (WES): Speeds processing of exome capture data through parallelized mapping and variant calling.
• Large dataset processing: Reduces runtime for computationally demanding sequencing analyses on multi-node clusters and multi-core machines.

Methodology:

Performs read mapping followed by variant calling according to GATK Best Practices and parallelizes these steps across multi-node and multi-core compute infrastructures.