MegaBOLT

MegaBOLT is a high-performance bioinformatics accelerator developed by Complete Genomics, designed to deliver ultra-fast, accurate, and user-friendly sequencing data analysis for whole genome sequencing (WGS) and whole exome sequencing (WES) workflows. Powered by a purpose-built ultra high-performance bioinformatics workstation, MegaBOLT incorporates industry-standard algorithms including SOAPnuke, Minimap2, BWA, GATK HaplotypeCaller, MuTect2, and DeepVariant, making it suitable for research and clinical laboratories seeking to accelerate genomic analysis without sacrificing sensitivity or precision.

MegaBOLT is built for laboratories that need to process large sequencing runs efficiently and cost-effectively, replacing the need for multiple servers with a single consolidated platform. It integrates seamlessly with Complete Genomics' proprietary LIMS (ZLIMS) and offers a graphical user interface that requires no command-line expertise or bioinformatics background.

MegaBOLT Analysis Pipeline

• Data QC: Raw FASTQ files are quality-controlled using SOAPnuke, producing a filtered FASTQ file and a Stats file.
• Read Mapping: Quality-controlled FASTQ files are aligned to a reference genome using Minimap2 (default) or BWA-Mem.
• Position Sorting: Aligned files undergo position sorting and duplicate marking to produce a BAM file.
• Base Quality Score Recalibration (BQSR): The sorted BAM file is processed through BQSR to improve basecall accuracy and optimise downstream variant calling results.
• Variant Calling: Germline or somatic variant calling is performed. The default caller is GATK 3.8 HaplotypeCaller (germline), with options to switch to GATK v4 (germline), MuTect2 (somatic), or DeepVariant (germline). This step identifies differences between the sample and the reference genome, producing Variant Calling Files (VCFs).
• Variant Quality Score Recalibration (VQSR): A final filtration step applied to VCF and gVCF files to ensure increased accuracy of variant calls before the final report is generated.

Speed and Performance

• Germline WGS at 30X coverage can be completed in just 1.5 hours — 28X faster than a traditional GATK pipeline.
• Germline exome analysis at 100X coverage is completed in 20 minutes — 47X faster than GATK for whole exome.
• Somatic WGS analysis at 40X coverage is completed in 5 hours; somatic whole exome at 400X coverage is completed in 50 minutes.
• MegaBOLT can analyse a full DNBSEQ-G400 sequencing run in a single day — a task that would take other processors up to two weeks.
• One MegaBOLT unit matches the output of 10 standard computers, eliminating the need for multiple servers and reducing both space and infrastructure costs.
• Annual analysis capacity supports up to 5,000 WGS (30X) runs per unit.

Variant Calling Accuracy

• MegaBOLT includes a deep learning variant calling module, MegaBOLT-DV, optimised through specialised algorithms and neural network model training.
• When used in combination with PCR-Free library preparation and DNBSEQ sequencing technology, MegaBOLT-DV achieves SNP precision of 99.9% and INDEL precision of 99% for human WGS variant calling.
• SNP results from 15X PCR-Free data processed with MegaBOLT-DV are comparable to GATK variant calling results from 30X PCR data, while INDEL performance is significantly better.

User Interface and LIMS Integration

• MegaBOLT integrates with Complete Genomics' proprietary ZLIMS for fully automated sequencing and analysis workflows.
• A graphical user interface (GUI) enables operation without command-line coding or a specialised bioinformatics background.
• Laboratory equipment management and real-time monitoring are supported.
• Sample information recording and tracking is built in.
• Data transmission and management capabilities are included.
• Analysis task scheduling and computing resources are managed within the platform.
• Management and visualisation of analysis results and reports are provided directly through the interface.

Workstation Specifications

• CPU: Intel Xeon Gold x2
• RAM: 192 GB DDR4
• HDD Storage: 30 TB
• SSD Cache: 2.25 TB
• License: 110 Tbp WGS/WES Basic Analysis Package
• Annual Analysis Capacity: Up to 5,000 WGS (30X) per set
• Included applications: ZLIMS Lite and ZMART
• Display monitor included

MegaBOLT is available as a hardware workstation server with an optional dongle, and software licenses are offered on an annual basis for WGS/WES Basic Analysis. Two analysis tiers are available: Basic (covering clean data processing through to variant calls) and Full (adding quality control and report generation steps). MegaBOLT is designed to integrate with Complete Genomics' broader sequencing ecosystem, including DNBSEQ sequencing platforms and associated library preparation kits.