This blog provides an overview of the five most popular Next-Generation Sequencing (NGS) sequencers, highlighting their unique technologies and applications. Illumina sequencers, dominating with 90% of the world’s sequencing data, use Sequencing by Synthesis (SBS) technology and offer a range of both benchtop and production-scale sequencers. Ion Torrent systems, launched in 2011, use semiconductor chips to read nucleotide sequences through pH changes, offering various instruments including the entry-level GeneXus system. MGISeq instruments utilize nanoball sequencing, a form of second-generation sequencing, and are noted for their high throughput and compatibility with Illumina protocols. Oxford Nanopore’s sequencers are known for their portability and flexibility, with products like the MinION making whole-genome sequencing more accessible and affordable. Lastly, PacBio HiFi sequencers employ single-molecule real-time (SMRT) sequencing, a third-generation technology known for long reads, low error rates, and faster processing compared to second-generation systems. Each of these sequencers has distinct features catering to different aspects of genomic research and diagnostics.
These popular sequencing vendors, spanning second-generation to fourth-generation sequencing technologies, currently dominate the NGS landscape.
- Illumina sequencers account for 90% of the world’s sequencing data. Illumina pioneered SBS technology utilizing fluorescence to read clonally amplified DNA templates attached to a glass flowcell. Illumina offers a range of sequencers broadly categorized into benchtop sequencers (iSeq 100, MiniSeq, MiSeq, and NextSeq) and production-scale sequencers. (NextSeq and NovaSeq). The company discontinued its popular HiSeq platform in 2021; it will be supported through 2024.
- Ion Torrent sequencers were launched in 2011 as a direct competitor to Illumina. Ion Torrent sequencers employ second-generation SBS technology. Instead of using fluorescence to read sequences, Ion Torrent systems read nucleotide sequences using a semiconductor chip that measures changes in pH caused by the release of hydrogen ions during DNA polymerization. IonTorrent offers four different instruments. The GeneXus system is an entry-level system offering an economical option for low-sample throughput. IonGeneStudio S5 systems come in five variants and can generate 2M to 130M reads and 0.3 to 50Gb data in a single run taking at most 21.5 hours. The PGM Dx is a low-throughput diagnostic system.
- MGISeq instruments employ a form of second-generation sequencing called nanoball sequencing. Not to be confused with nanopore sequencing, SMS, MGI sequencers use rolling circle replication to amplify small fragments of genomic DNA into DNA nanoballs. The nanoballs are adsorbed onto a sequencing flow cell, and the sequencer reads the sequence using fluorescence. Aspects of the technology resemble Illumina technology, and in fact, MGI sequencers can accept sequencing libraries developed using Illumina protocols. The DNBSEQ-T7 has been reported to sequence up to 800,000 samples per year using an automated library preparation system that can operate for 24 hours without human intervention. MGI sequencing suffers from the same disadvantages as other short-read sequencing techniques and cannot resolve structural variants or distinguish highly homologous genomic regions. These instruments will likely gain more traction now that they are being marketed in the US and Europe.
- Oxford Nanopore markets its sequencers as portable and flexible, giving even the smallest labs access to NGS capabilities. Nanopore sequencing has made whole-genome sequencing faster and less expensive. It can also be used in conjunction with second-generation sequencing technology to identify the order of nucleotides in fixed cells and tissues. Oxford Nanopore released its first sequencer, the MinION, in 2014. It has since released the GridION Mk1 and the PromethION 24/48.
- PacBio HiFi sequencers use single-molecule real-time (SMRT) sequencing, a third-generation sequencing technology introduced in 2010. SMRT uses zero-mode waveguides (ZMWs) embedded on a chip. Each ZMW holds a single molecule of single-stranded DNA template, enabling scientists to visualize and monitor the activity of DNA polymerase in real time as synthesis occurs. SMRT can generate long reads at a low error rate and much faster than second-generation systems.
