MegaBOLT Bioinformatics Pipeline

Experience Lightning-Fast Analysis

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Bioinformatics accelerator for high-speed sequencing analysis

Powered by our ultra high-performance bioinformatics computer, MegaBOLT incorporates classical algorithms like SOAPnuke, Minimap2, BWA, GATK HaplotypeCaller + MuTect2, DeepVariant, and more to deliver ultra-fast speed, excellent sensitivity and precision, and easy, user-friendly operation for your WGS and WES sequencing analysis.

MegaBOLT Pipeline

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  • Data QC: Raw FASTQ files are QC’d using SOAPnuke to generate a filtered FASTQ file and Stats file​.
  • Read Mapping: QC’d sample FASTQ files are aligned to a reference genome using Minimap2 (default) or BWA-Mem.
  • Position Sorting: The aligned sample files go through position sorting and duplicate marking steps resulting in a BAM file.
  • BQSR: The sorted BAM file then goes through base quality score recalibration (BQSR), to create a BAM file with increases basecall accuracy for best Variant Calling results​.
  • Variant calling: Germline or Somatic Variant Calling is preformed where the default Variant Caller is GATK3.8 HaplotyperCaller (germline), but can be changed to GATK v4 (germline), Mutect2 (somatic) or DeepVariant (germline). The goal is to find where the sample differs from the reference genome or where variation occurs. This step produces Variant Calling Files (VCFs).​
  • VQSR: The last step before the final report is Variant Quality Score Recalibration (VQSR). Like BSQR, it is variant filtration step to ensure increased accuracy for the variant calls in the VCF and gVCF files.

Up to 36X Faster Than Traditional GATK Pipeline

MegaBOLT can perform Germline WGS in 1.5 hrs at 30X coverage and Germline Exome analysis at 100X in 20 mins. That’s 28X faster than GATK for whole genome and 47X faster than GATK for whole exome.​ Similarly, for Somatic analysis, MegaBOLT can complete the analysis in 5 hours for whole genome at 40X and in 50 minutes for whole exome at 400X coverage. These numbers are for processing a whole sequencing run by one MegaBOLT. For reference, MegaBOLT can analyze DNBSEQ-G400 data in one day, a task would take other processors up to 2 weeks.

Basic includes the analysis steps from clean data after quality control to variant calls, where Full includes extra steps of quality control and report generation.

One MegaBOLT Equals Multiple Servers

Only one MegaBOLT is all you need for storage and analysis. This consolidated computing power translates to a huge cost savings on both space and funds since you don’t need multiple servers or storage to complete analysis tasks.

MegaBOLT matches the output of 10 normal computers in a single platform.

User-Friendly Interface and Multi-Task Scheduling

MegaBOLT is integrated with our proprietary LIMS (ZLIMS) for fully automated sequencing and analysis, and a friendly graphical user interface (GUI) means command line codes or a bioinformatics technical background are not required.

  • Laboratory equipment management and real-time monitoring
  • Sample information, recording and tracking
  • Data transmission and management
  • Analysis task scheduling and computing
  • Management and visualization of analysis results and reports

Achieve 99.9% Accuracy for SNP and INDEL Variant Calling

MegaBOLT is equipped with a deep learning module for variant calling, MegaBOLT-DV, which is optimized by algorithms and specified neural network model training. When MegaBOLT-DV is used in combination with PCR-Free library preparation and DNBSEQ sequencing technology, the human WGS variant calling precision can reach an excellent SNP 99.9% and INDEL 99%.

Compared with the GATK variant calling results of 30X PCR data, SNP of 15X PCR-Free data from MegaBOLT-DV is comparable and INDEL is far better.

MegaBolt Workstation Specifications

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ComponentTech Specs
CPUIntel Xeon Gold x2
Display MonitorIncluded
RAM192 GB DDR4
HDD Storage30 TB
SSD Cache2.25 TB
License110 Tbp WGS/WES Basic Analysis Package
Annual Analysis CapacityUp to 5,000 WGS (30X)/set
AppsZLIMS Lite
ZMART

Ordering Information

Type​Product name​Catalog No.​
HardwareMegaBOLT Bioinformatics Accelerator (Workstation Server)900-000677-00
HardwareMegaBOLT Dongle058-000019-00
SoftwareMegaBOLT WGS/WES Basic Analysis License (1 year duration)970-000136-00

Learn More

Download the brochure or talk to a specialist to get started with MegaBOLT.

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