Advanced Sequencing Data Analysis with MGI BIT Platforms
As sequencing technologies and data analysis tools continue to advance, it has become increasingly important to ensure that sequencing data is handled accurately and efficiently. Modern sequencing platforms are capable of diverse tasks, including genome assembly, transcript quantification, and interpretation of complex experiments. To support these capabilities, MGI has developed a range of internationally competitive Bioinformatics Technology (BIT) products, including MegaBOLT, ZBOLT and ZBOLT Pro.
Insights from MGI Senior Vice President Dr Ming Ni
MGI Senior Vice President Dr Ming Ni shared insights into these platforms in his interview with SEQanswers.
Quality Control of Sequencing Data
NGS differs from traditional industries because the quality of sequencing data underpins all downstream applications. MGI and Complete Genomics maintain rigorous quality control across nearly all sequencing steps:
- Sequencing Strategy: Using DNA nanoball technology minimises PCR cycles, reducing the risk of copying errors.
- Automation: Reduces manual operations in the lab, improving reproducibility.
- Data Analysis: SOAPnuke software, integrated into MegaBOLT, applies metrics such as Q30, GC content, and adapter contamination to ensure only high-quality data is processed. Parameters are flexible to suit different project requirements.
- Workflow Management: End-to-end systems cover sample submission, laboratory operations, data analysis, and reporting, ensuring fully automated, one-stop sequencing and analysis.
Key features include:
- Comprehensive Data Filtering and Visualization: Raw data is filtered using SOAPnuke to remove low-quality reads and adapters, with detailed Q30 and base quality visualizations for better insight.
- Flexible Parameter Adjustment: Users can set parameters specific to their libraries and sequencing runs to optimise downstream analysis.
- Accelerated QC Process: A streamlined pipeline with parallel processing ensures rapid quality assessment of large datasets.
Evaluating Assemblies and Alignments
MGI ensures reliability throughout the data lifecycle:
- Unified Task Scheduling: Automatic analysis software verifies result integrity and supports re-analysis for fault tolerance.
- Key Indicators: Metrics like mapping rate, coverage, and variant calling accuracy are compared to gold standards such as GATK best practices.
- Multiple Alignment Tools: Users can choose tools prioritising precision or sensitivity based on their project needs.
Transcript Quantification and Differential Expression
MegaBOLT supports resource-intensive analyses using pipelines based on GATK best practices. RNA-seq outputs standard gene expression matrices, supporting downstream analyses like heatmaps, clustering, and differential expression. Tools compatible with these matrices include DEGseq, DEseq, edgeR, EBseq, NOIseq and PoissonDis.
Visualization Tools
MGI’s ZTRON series provides visualization across the entire NGS workflow, including sample management, laboratory operations, data analysis, and reporting. Users can schedule analyses, monitor progress, manage data securely, and customise bioinformatics pipelines through a drag-and-drop interface. Tools like samtools and IGV enable detailed inspection and visualization of variant calling results.
Trends in Sequencing Data Analysis
1. Large-Scale Trans-Omics Datasets: MegaBOLT/ZBOLT/ZBOLT Pro accelerators deliver up to 70,000 WGS per year, with daily throughput reaching 20TB of genomic data. ZTRON integrates storage, computing, and management for large populations.
2. Data Security and Management: MGI products follow “Privacy by Design,” complying with regulations such as GDPR, HIPAA, and China’s Data Security Law, ensuring secure storage, transmission, and processing of genomic data. ZLIMS laboratory management provides full-process oversight from samples to results.
3. AI Integration: MegaBOLT-DV uses deep learning for variant calling. Future integrations with models like GPT-4 will further improve analysis efficiency and accuracy.
Accuracy and Reproducibility
- QC preprocessing, T2T genome comparison, and AI algorithms enhance accuracy.
- Reproducibility is ensured by controlling random functions and down-sampling operations during mutation detection, allowing consistent results across analyses.
MGI’s BIT platforms, combined with its sequencing instruments, provide a fully integrated ecosystem for high-throughput, secure, and reproducible genomic data analysis.
*Unless otherwise informed, StandardMPS and CoolMPS sequencing reagents, and sequencers for use with such reagents, are not available in Germany, Spain, the UK, Sweden, Italy, the Czech Republic, Switzerland and Hong Kong (CoolMPS is available in Hong Kong).
*Products are for Research Use Only. Not for use in diagnostic procedures, unless otherwise specified.
