Fast and cost-effective whole-genome analysis

Overview

Whole-genome sequencing (WGS) plays a critical role in modern genomics research, enabling the identification of genetic variants associated with diseases and therapeutic responses. However, analyzing large batches of high-coverage sequencing data requires scalable pipelines that ensure accuracy, efficiency, and cost optimization.

Excelra collaborated with a client to develop a fast and cost-effective whole-genome analysis pipeline capable of processing high-coverage sequencing datasets while identifying aggregated rare variants linked to genomic associations. By leveraging advanced Bioinformatics Solutions, Computational Biology Services, and Scientific Informatics, Excelra delivered a scalable solution aligned with industry best practices for genomic analysis.

Our client

The client partnered with Excelra to build an efficient whole-genome variant calling pipeline capable of analyzing large batches of sequencing data. Their research required the rapid processing of 50X whole-genome sequencing samples while identifying associations driven by aggregated rare variants.

Client’s challenge

Processing high-coverage whole-genome sequencing data presents multiple challenges:

• Managing large volumes of sequencing reads from multiple samples
• Performing accurate detection of diverse variant types
• Ensuring reproducibility across large genomic datasets
• Identifying associations through aggregated rare variant analysis
• Maintaining cost-efficiency while scaling computational workflows

The client required a robust genomic pipeline capable of handling these challenges while delivering accurate and reproducible results.

Client’s goals

The key objective was to develop a cost-efficient whole-genome variant calling pipeline that could:

• Process large batches of 50X WGS samples efficiently
• Detect multiple variant types including SNVs, Indels, SVs, and CNs
• Perform aggregated rare variant analysis to identify genomic associations
• Ensure reliable variant discovery with stringent quality control
• Scale analysis pipelines for high-throughput genomic studies

Our approach

Excelra developed a comprehensive genomic analysis pipeline that integrated best-in-class tools and workflows.

Read alignment and variant calling

The pipeline incorporated accurate read alignment followed by variant detection across multiple variant types including:

• Single nucleotide variants (SNVs)
• Insertions and deletions (Indels)
• Structural variants (SVs)
• Copy number variants (CNs)

This ensured comprehensive variant detection across the genome.

Joint genotyping and quality control

Excelra implemented joint genotyping workflows along with extensive quality control checks to maintain accuracy and reliability across large sample batches.

Advanced pipeline architecture

The solution leveraged Excelra’s Hg38 HLA and ALT-aware genomic pipeline, aligned with Broad Institute’s GATK best practices for variant discovery. This architecture enabled precise genomic analysis even in complex genomic regions.

Scalable bioinformatics infrastructure

By integrating scalable data processing workflows and automated analysis pipelines, Excelra ensured that the platform could process large sequencing datasets efficiently.

These approaches align with modern genomics analysis techniques discussed in bioinformatics solutions and techniques for data-driven discoveries.

Results

Excelra successfully delivered a scalable pipeline that significantly improved whole-genome analysis efficiency.

Key outcomes

• Built a pipeline capable of annotating up to 150 high-coverage 50X WGS samples
• Enabled accurate detection of multiple genomic variant types
• Accelerated variant discovery for large genomic datasets
• Reduced computational cost while maintaining analytical accuracy
• Supported identification of genomic associations through aggregated rare variants

Key benefits

• High-Throughput genomic processing
  The pipeline efficiently processes large batches of high-coverage sequencing data.
• Accurate variant discovery
  Integrated variant detection across SNVs, Indels, SVs, and CNs ensures comprehensive genomic analysis.
• Cost-Efficient infrastructure
  Optimized workflows reduce computational costs while maintaining scalability.
• Faster genomic insights
  The solution accelerates discovery of genomic associations and variant analysis.