The Throughput Paradox: Why Next-Generation Sequencing Bottlenecks Persist Beyond the Sequencer

Joe Mellor
Joe Mellor, PhD
CSO, Co-founder
seqWell

The landscape of next-generation sequencing (NGS) continues to be defined by astonishing technological progress. We continue to witness sequencer throughput expansion with systems like the Illumina NovaSeq™ X+ and Ultima Genomics UG100™ in the short-read space, as well as the PacBio Revio™ and Oxford Nanopore PromethION® in the long-read space. Surprisingly, even with these profound advances, overall throughput and scalability of genomics remained a central challenge for the scientific community in 2025.

This seeming paradox stems from a critical shift: the bottleneck has migrated from sequence throughput to library preparation throughput. While the sequencers themselves act as powerful engines, the increasing complexity and limitations inherent in upstream sample handling and NGS library chemistry continue to hold back the capacity to…
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