Method of the Year 2022: Long-read sequencing

Long-read sequencing powers a more complete reading of genomic information.

To large-scale projects and individual labs, long-read sequencing has delivered new vistas and long wish lists for this technology’s future.

The year 2022 will be remembered as the turning point for accurate long-read sequencing, which now establishes the gold standard for speed and accuracy at competitive costs. We discuss the key bioinformatics techniques needed to power long reads across application areas and close with our vision for long-read sequencing over the coming years.

Advances in long-read sequencing technologies have broadened our understanding of genetic variation in the human population, uncovered new complex structural variants and offered an opportunity to elucidate new variant associations with disease.

Long-read sequencing has become a widely employed technology that enables a comprehensive view of RNA transcripts. Here, we discuss the importance of long-read sequencing in interpreting the variables along RNA molecules, such as polyadenylation sites, transcription start sites, splice sites and other RNA modifications. In addition, we highlight the history of short-read and long-read technologies and their advantages and disadvantages, as well as future directions in the field.

As long-read sequencing technologies continue to advance, the possibility of obtaining maps of DNA and RNA modifications at single-molecule resolution has become a reality. Here we highlight the opportunities and challenges posed by the use of long-read sequencing technologies to study epigenetic and epitranscriptomic marks and how this will affect the way in which we approach the study of health and disease states.

Long-read sequencing has made closed microbial genomes a routine task, and the dramatic increase in quality and quantity now paves the way to a complete microbial tree of life through genome-centric metagenomics.

In vitro models and single-cell atlases help uncover the mysteries of human embryogenesis.

The combination of microscopy, targeted illumination and single-cell sequencing is driving applications from direct evolution to spatial omics.

CRISPR systems can be leveraged to direct recombinases to integrate gene-sized DNA sequences.

Computational approaches are pushing the limits of unknown metabolite annotation.

Data integration methods weave genomics data into holistic pictures of biological systems.

Strategies to overcome poor reproducibility in MRI studies are needed.

Advances in fluorescence microscopy and spectroscopy show their promise for applications that complement in situ structural biology methods like cryoelectron tomography.

Mechanoimmunology methods help dissect the mechanical forces within the immune system.