Next-Generation Sequencing Technology Update

Sequencing a genome is now cheaper, more accurate, and informative than ever. Innovation is at the core of these improvements, which are transforming NGS technologies. In this article, we will cover the latest advances in this rapidly evolving field, exploring how improved accuracy, throughput, and price are redefining NGS.

Short-read sequencing dominance

Short‑read sequencing remains the backbone of clinical and large‑scale population genomics. This dominance is mainly due to low error rates and high coverage, affordable costs, and extensive validation across clinical settings.

Illumina NovaSeq X Series

At the center of Illumina’s latest advances is the NovaSeq X Series. The XLEAP-SBS chemistry incorporates more stable reversible‑terminator nucleotides and improved polymerase fidelity, reducing phasing and miscalls errors. Together with upgraded Q-score recalibration, >85% of bases fall in Q30, with faster cycle times. This enables more confident rare‑variant and MRD calling at routine depths.

In terms of throughput, NovaSeq X can produce up to 8 Tb with a 25B flow cell, doubling on NovaSeq X Plus, where two flow cells can run at once. This represents roughly a 2–3x increase over NovaSeq 6000. This is achieved through better optics and imaging, allowing better cluster detection and thus higher nanowell density. Combining higher accuracy with increased output, sequencing costs are reduced to $200 per genome.

Illumina’s platforms also support integrated epigenetic analysis. The newly launched 5-base solution steps away from bisulfite technologies, reducing time and allowing variant calling in the same run by relying on enzymatic conversion of methylated cytosines.

Ultima Genomics

Ultima Genomics recently entered the short-read sequencing scene as a cost-disruptor. After coming out of stealth mode in 2022, they claimed a human genome could be sequenced for $100 on the UG 100 platform. This number has been further reduced to $80 with the introduction of Solaris chemistry in 2025.

According to David Peoples, Chief Financial and Business Officer at Ultima Genomics, the largest factor contributing to such a cost reduction “comes from moving away from conventional flow cells onto large open-surface semiconductor wafers, which are produced at very low cost by the semiconductor industry.” This is coupled with a sequencing chemistry that “is fast and makes efficient use of expensive labeled nucleotides and enzymes,” alongside automated, fab-style instrument operation designed for continuous 24/7 sequencing.

Unlike Illumina’s SBS, Ultima Genomics’ chemistry introduces one nucleotide type per cycle. The nucleotides are un-terminated with only a fraction being fluorescently labeled, which increases sequencing speed, reduces costs, and lowers substitution and phasing errors. As Peoples mentioned, “more than 75% of flows are above Q30, and more than 85% of base substitutions are above SNVQ40.” Their technology addresses homopolymer challenges. By incorporating optical endpoint detection and deep-learning basecalling, their platform can accurately call homopolymers up to 12 bases in length.

Ultima further extends its SNV accuracy to rare-variant and low-input applications, including liquid biopsy and MRD, using its proprietary ppmSeq technology. Peoples explained that: “ppmSeq avoids denaturing the duplex DNA templates before amplification, allowing direct consensus reading of both strands in a single sequencing step without the yield losses of in-silico strand pairing.” Through duplex error correction, Ultima Genomics reports the detection of SNVs with at least part per million accuracy (SNVQ60+).

Long-read sequencing expansion

Recent advances in long-read sequencing platforms are closing the accuracy and price gap with short-read technologies, making the advantages of longer reads more accessible to daily workflows.

Pacific Biosciences

Since PacBio introduced HiFi reads back in 2019, per-base accuracy for human genomes has reached 99.9%. However, prices have remained high, with the Revio system delivering a 30x human genome at around $1,000. As Aaron Wenger, Sr. Director of Product Management at PacBio, explained: “The primary cost driver is the SMRT Cell, so PacBio has focused on increasing data output per cell through chemistry and compute improvements.”

SPRQ chemistry, launched in 2024, incorporates optimized loading reagents and a new polymerase that allows more DNA molecules to effectively attach to nanowells (ZMWs). This polymerase has shown higher stability and processivity, performing more passes on circularized DNA templates. Altogether, as Wenger stated, “yield increased from approximately 90 Gb to 120 Gb per SMRT Cell,” contributing to a price drop to around $500 per genome. Following this cost-reduction logic, PacBio’s latest SPRQ-Nx chemistry, still in beta, will allow the reuse of SMRT cells 2 to 3 times, “enabling a list price of approximately $350 per genome,” Wenger added.

By combining these advances with parallel cells and DeepConsensus, Revio increases output to up to 480 Gb per run, compared with 30 Gb on the previous Sequel IIe. These improvements also extend to epigenetic readouts. According to Wenger, PacBio now plans to further improve accuracy for both 5mC and 6mA and add support for 5hmC. This will be implemented with HK2, a deep learning model that combines local polymerase kinetic signals with long-range sequence context along each read.

Together, these advances broaden the clinical applications of long-read sequencing. As Wenger stated, “the most important aspect that SPRQ chemistry brings to clinical applications is the reduction of DNA input requirements by fourfold,” down to 500 ng. This opens access to neonatal samples and large population studies based on saliva samples.

Oxford Nanopore Technologies

Oxford Nanopore has focused on increasing accuracy through advances in pore chemistry and basecalling. By introducing a dual-reader nanopore, R10.4.1 flow cells capture more positional information, increasing the resolution of homopolymers and other difficult motifs. Coupled with a more stable motor enzyme and reagents with Kit 14, translocation speed is more controlled and slower. These advances make raw signals richer in context, and together with Dorado’s deep learning base caller, help increase accuracy above Q20, with duplex models reaching Q30.

In terms of throughput, PromethION 24/48 can host 24 or 48 high-density flow cells in the same instrument. Each cell harbors thousands of nanopores running in parallel, delivering 200 Gb of data per cell, pointing to a potential multi-terabase output from these instruments. These advances support reductions in cost, but the biggest promise for affordable ultra-long reads comes from the PromethION Plus flow cell, still in early access. ONT targets a per-genome price around $345 per 30x genome by removing flow washes and increasing output per cell.

Improvements in accuracy and cost are making ultra-long sequencing increasingly relevant for clinical adoption, where rare disease and cancer genomics can benefit from resolving long and complex variants, together with methylation patterns.

Emerging paradigms

The latest NGS innovation belongs to Roche. Their new technology, sequencing by expansion (SBX), converts DNA information into a much larger synthetic polymer called Xpandomer. Then, it is read out electrically as it passes through nanopores on a CMOS sensor array. “The technology has the flexibility to support short and longer reads,” said Josh Lauer, Head of the Molecular Labs Customer Area at Roche Diagnostics. “The longer read lengths (up to 1500 bp) are designed to better span and characterize complex repeat regions compared to traditional short-read sequencing.”

The SBX technology has been presented, but the AXELIOS 1 platform has not been commercialized yet. Available data highlights superior performance for certain applications, such as significantly faster sequencing speeds. As Lauer mentioned, “The fastest sample to VCF time has been achieved at <4 hrs via SBX-Fast.” The price is also a hot topic, with limited data currently available. With more data coming through during 2026 and 2027, time will tell how much and for what applications SBX outshines other NGS technologies.

NGS advances are pushing the field to lower prices, higher accuracy, and better throughput. Short-read technologies remain central in clinical settings, while long-read platforms are reducing historical limitations in accuracy, offering more competitive pricing and increasingly robust epigenomic profiling. Together with emerging technologies, these advances show a fast-evolving NGS landscape, with ongoing innovation reshaping how sequencing is applied.