Short Read Sequencing Overview

Short read sequencing at MGI GTAC@MGI supports high throughput DNA sequencing studies using Element Biosciences AVITI™ and Illumina® platforms, with workflows designed for scale, reproducibility, and analysis ready outputs. Projects range from targeted panels to population scale whole genome and whole exome sequencing, with execution aligned to study design and downstream objectives.

  • Illumina® sequencing performed on NovaSeq™ X Plus for cohort scale and production runs.
  • Support for whole genome, whole exome, targeted DNA sequencing, methylation, and sequencing only submissions.
  • Run planning, pooling strategy, and depth optimization matched to study goals and budget.
Short read sequencing workflow at GTAC@MGI

Short Read Sequencing Platforms and Deliverables

Platforms

Sequencing Systems

  • Illumina NovaSeq X Plus
  • Illumina i100
  • Element AVITI
Supported material

Sample types

  • DNA extraction available for numerous specimen types
  • Genomic DNA from blood, saliva, or tissue (fresh frozen or FFPE)
  • Customer prepared libraries for sequencing only projects
Data outputs

Deliverables

  • FASTQ files generated to project specifications
  • DRAGEN Bio-IT alignment and variant processing available when requested
  • 10x Genomics® standardized analysis pipelines

Short Read Sequencing Services

Choosing the right DNA sequencing strategy

Whole Genome Sequencing

Use when genome-wide context matters

  • Unbiased detection of all major variant classes
  • Structural and copy number variation at scale
  • Rare disease, cancer, and population studies
Whole Exome Sequencing

Use when coding variation is the focus

  • Protein-altering variants in germline or somatic studies
  • Cost-efficient designs for moderate to large cohorts
  • Family, trio, and clinically oriented analyses
Targeted DNA Sequencing

Use when depth and specificity are required

  • Defined genes, pathways, or hotspot regions
  • Ultra-deep coverage for low-frequency variants
  • Large cohorts with focused biological questions
Methylation Sequencing

Use when epigenetic modifications are of interest

  • Provides CpG methylation levels (percent methylation per site)
  • Differentially methylated regions (DMRs)
  • Cell-type or disease-specific methylation patterns

These examples reflect common use cases. Final study design depends on sample type, cohort size, and downstream analysis goals.

Short Read Sequencing Instrumentation

Illumina NovaSeq X Plus

Illumina® NovaSeq™ X Plus

High throughput short read sequencing system optimized for large scale WGS, WES, and multi omic studies.

  • Improved accuracy and lower error rates compared to prior systems
  • Ideal for population scale genomics, high throughput WES, and large cohorts
  • Up to 8 Tb total output per 25B flow cell
  • Up to 72 human whole genomes per 25B flow cell (30×)
  • 150 bp paired end sequencing with advanced XLEAP SBS™ chemistry
  • 10B, 5B, 1.5B flow cells available for variable project size and read lengths
Illumina MiSeq i100 benchtop short read sequencing system

Illumina® MiSeq™ i100

Benchtop short read sequencing system optimized for fast, flexible sequencing and longer read applications.

  • Flexible run configurations
  • Longer reads available up to 2×300 bp
  • Faster turnaround time for small projects
  • Spike ins available for 2×150 and 2×250 sequencing runs
Element Biosciences AVITI short read sequencing system

Element Biosciences® AVITI®

High accuracy short read sequencing system powered by avidity chemistry for flexible transcriptomic workflows.

  • Flexible run configurations
  • Longer reads (2x300) available
  • Faster turnaround time for small to mid-sized projects
  • Excellent base quality with lower duplication rates
  • Lower index hopping rates