MiSeq i100 Plus Arrives at SA Genomics - Features and Applications

In late November 2025, the SA Genomics Centre expanded its NGS capabilities with the addition of the Illumina MiSeq i100 Plus. Compact, fast, and versatile, this system is purpose-built for small-scale and targeted sequencing, enabling rapid results while maintaining the high data quality our clients rely on.

The MiSeq i100 Plus brings the next generation of accessible sequencing to our facility, with room-temperature reagents, onboard secondary analysis, and flow-cell configurations ranging from 5M to 100M reads, making it a powerful fit for a wide range of genomics applications.

Key Applications

The MiSeq i100 Plus is optimised for projects requiring moderate throughput and high accuracy. Popular applications include:

Targeted Amplicon Studies

Perfect for 16S/ITS profiling, amplicon-based disease panels, and genotyping, the system provides fast run times ideal for iterative studies or multi-batch analysis.

Plasmid and Small Genome Sequencing

High-accuracy paired-end reads (up to PE300 and PE500) allow efficient sequencing of:

• Plasmids
• Viral genomes
• Bacterial genomes
• CRISPR-edited constructs

This makes the platform a great fit for synthetic biology, microbial engineering, and genome-editing confirmation.

Microbial Genomics & Metagenomics

The instrument supports:

• Small whole-genome sequencing
• Shotgun and shallow shotgun metagenomics
• Immune repertoire profiling

These capabilities help researchers explore community composition, strain-level diversity, and low-biomass samples with confidence.

QC and Library Validation

The rapid workflows are also suited for:

• Library QC
• Pilot-scale transcriptomics
• Quality screening prior to high-throughput sequencing

Flow-Cell Configurations at a Glance

The MiSeq i100 Plus offers four flow-cell sizes to match project scale and budget:

Actual output may vary depending on library prep method and sample type.

This flexible range enables cost-effective sequencing for both small pilot runs and larger, more complex projects.

Key Features to Highlight

• Fast run times – up to 4× faster than earlier MiSeq models
• Room-temperature reagents – simplified handling and logistics
• Onboard secondary analysis – quick access to demultiplexing, alignment, and reporting
• Flexible read lengths – from SE100 to PE500, covering everything from QC to complete microbial genomes

Reach Out About Your Next Project

Whether you're exploring microbial diversity, validating genome edits, sequencing plasmids, or running targeted panels, the MiSeq i100 Plus offers performance and flexibility ideal for small-to-medium genomics workloads.

Reach out to us to set up a time to discuss how the MiSeq i100 Plus can support your research.

Helpful Links

• MiSeq i100 Overview
• MiSeq i100 Specifications
• MiSeq i100 Brochure
  
• SAGC Microbial Profiling Service