MegaBOLT

The MegaBOLT Bioinformatics Pipeline offers a high-speed solution for sequencing analysis, utilizing an ultra high-performance computer to deliver rapid results with excellent sensitivity and precision. It incorporates classical algorithms such as SOAPnuke, Minimap2, BWA, GATK HaplotypeCaller, MuTect2, and DeepVariant, making it suitable for whole genome sequencing (WGS) and whole exome sequencing (WES) analysis.

MegaBOLT Pipeline

The pipeline begins with data quality control, where raw FASTQ files are processed using SOAPnuke to produce filtered FASTQ and Stats files. Subsequently, the quality-controlled FASTQ files are aligned to a reference genome using Minimap2 or BWA-Mem. The aligned files undergo position sorting and duplicate marking, resulting in a BAM file. Base quality score recalibration (BQSR) is then applied to enhance basecall accuracy, optimizing variant calling results.

Variant calling is performed using GATK3.8 HaplotyperCaller for germline variants, with options to switch to GATK v4, Mutect2 for somatic variants, or DeepVariant for germline variants. This step identifies differences between the sample and reference genome, producing Variant Calling Files (VCFs). The final step involves Variant Quality Score Recalibration (VQSR) to ensure high accuracy in the variant calls.

Performance and Efficiency

MegaBOLT is significantly faster than traditional GATK pipelines, performing germline WGS at 30X coverage in 1.5 hours and germline exome analysis at 100X in 20 minutes. It is 28 times faster for whole genome and 47 times faster for whole exome analysis compared to GATK. For somatic analysis, it completes whole genome analysis at 40X in 5 hours and whole exome at 400X in 50 minutes. A single MegaBOLT can handle tasks that would typically require multiple servers, offering substantial cost savings in space and resources.

User-Friendly Interface

Integrated with a proprietary Laboratory Information Management System (LIMS) called ZLIMS, MegaBOLT provides a fully automated sequencing and analysis experience. Its graphical user interface (GUI) eliminates the need for command line codes or extensive bioinformatics expertise, facilitating ease of use.

Accuracy and Specifications

Equipped with a deep learning module, MegaBOLT-DV, the system achieves 99.9% accuracy for SNP and 99% for INDEL variant calling when combined with PCR-Free library preparation and DNBSEQ sequencing technology. The workstation features Intel Xeon Gold CPUs, 192 GB DDR4 RAM, 30 TB HDD storage, and a 2.25 TB SSD cache, supporting up to 5,000 WGS analyses annually.

For more information, users can download the brochure or contact a specialist to explore MegaBOLT's capabilities further.