A Comparative Analysis of Short Read Sequencing Platforms for Metagenomic Applications

Inquiries about the best sequencer for metagenomic Next-Generation Sequencing (mNGS) are common among our customers. While the answer depends on specific requirements, we’ve conducted an in-depth analysis to aid in your decision-making process.

A Brief Historical Context: Sanger sequencing, known as the first-generation method, sequences DNA post-synthesis. Despite the label “Next-generation Sequencing (NGS),” the advent of sequencing by synthesis technology for commercial use emerged around 2005. For two decades, the market was dominated by Thermo Fisher with Ion Torrent and Illumina, offering a variety of machines. Illumina utilizes a fluorescent tag to identify nucleotide bases added to the DNA strand, while Ion Torrent detects hydrogen release during nucleotide base addition, conducting both sequencing and synthesis concurrently.

Today, there are more short read manufacturers on the market, from Element Biosciences, Complete Genomics/MGI, to Singular Genomics and Ultima Genomics. First, we provide a very brief overview of the new entrants then we compare the options for a variety of mNGS applications. 

Complete Genomics/MGI, with over a decade of global market presence, employs rolling circle replication (RCR) to mitigate clonal errors and index hopping, thereby enhancing accuracy. Conceptually, their rolling nanoball technology enables dual sequencing by synthesis. Their product range and instruments offer diverse outputs suitable for various applications, with enhanced speed due to DNBSeq technology.

Element Biosciences‘ Aviti, a benchtop sequencer, tackles pre-facing or facing errors through specialized chemistry. The platform’s patented technology and unique chemistry bolster sequencing read accuracy and quality.

The G4 from Singular Genomics addresses flexibility and scalability needs with the capability to accommodate up to four flow cells simultaneously. This versatility enables users to tailor sequencing setups for different projects or output requirements, optimizing resource allocation.

Ultima Genomics‘ UG 100, a high-output, large-scale instrument, boasts a distinctive feature—no flow cells. Sequencing reactions, synthesis, and signal detection occur on a wafer, accompanied by automation to minimize manual intervention. Their PDM sequencing chemistry enhances accuracy, particularly in detecting single nucleotide variants at low frequencies, beneficial for oncological applications, especially utilizing cell-free DNA with minimal input and mutation frequencies.

Metagenomic Applications

For research and for clinical applications the priority of the features are slightly different. For clinical use accuracy, flexibility and turnaround times may be more important than in research settings. We evaluated the benchtop sequencers with medium output that are most appropriate for metagenomic analysis along several dimensions: 

  • Quality of the sequencing reads
  • Mapping quality
  • Total output
  • Flexibility
  • Speed
  • Cost (capital expenditure and operating expenses)


However, it’s essential to note that while selecting the sequencer is pivotal, achieving metagenomic goals also hinges on assay selection and the utilization of automation instrumentation. At Micronbrane Medical, we focused on developing technologies that overcome the barriers to ubiquitous adoption of mNGS in all settings.  Our Pathogen Real-Time Identification by Sequencing (PaRTI-Seq) assay and our PaRTI-Cular bioinformatic pipeline is revolutionizing infectious disease study, diagnosis and tracking from sample collection to definitive action.