Table 1.

Summary of the main advantages of long-reads sequencing over short-read sequencing.

Short-Read Technologies	Long-Read Technologies
Fixed run time: - Increased time to results and inability to identify workflow errors before completed sequencing - Additional practical complexities associated with handling and storing large volumes of sequence data	Real-time data acquisition: - Achieve rapid turnaround with immediate access to results - Enrich single targets during sequencing, with no additional sample prep using adaptive sampling - Identify microbiome composition and resistance in real-time
Limited flexibility: - Sample batching often required for optimal efficiency - Potentially leads to long turnaround times - Benchtop devices confine sequencing to centralized locations	Scalable and flexible: - Scale to suit the throughput needs - Decentralize sequencing - No sample batching needed
Read length typically 50–300 bp	Unrestricted read length (>4 Mb achieved)
Limited genomic characterization: - Short reads do not span entire structural variants or important classes of genomic aberrations (repeat expansions and repeat-rich regions) - fragmented genome assemblies and ambiguous isoforms identification - Short sequencing reads may not span complex genomic regions such as genes duplications, transposons and prophage sequences - Potentially missing important genomic information	Comprehensive genomic characterization: - Identify mutations in complex and repetitive genomic regions - Accurately phase single nucleotide variants, structural variants, and base modifications - Can fully assemble genomes more easily - Simplify de novo assembly and correct microbial reference genomes - Possibility to completely assemble genomes and plasmids from metagenomic samples - Resolving complex genomic regions and similar species
Amplification required: - Amplification can introduce bias reducing uniformity of coverage and removes base modifications - Necessitating additional sample prep and sequencing runs	Amplification-free protocols: - Detect and phase base modifications as standard - No additional preparation required
Constrained to the lab: - Traditional sequencing technologies are typically expensive and require substantial site infrastructure - Usually limited its usage to well-resourced environments - Delay in transmitting the results	Sequence anywhere: - Sequence in your lab or in the field - Sequence at sample source and eliminate sample shipping delays - Scale-up with high-throughput