Table 1. Pros and cons of four major HTS technologies

Technology	Pros	Cons
Illumina sequencing	• Widely used, with a large user base and well-established protocols. • High-throughput, with the ability to gen erate a large amount of data in a single run. • Low cost per base, making it the most cost-effective option for many applications.	• Read lengths are shorter compared to other techniques, typically 150–300 base pairs. • Limited accuracy for longer read lengths and lower accuracy for genomic regions with high GC content.
ThermoFisher’s Ion Torrent	• High-throughput with a large number of reads generated in a single run. • Lower cost per base compared to other technologies. • Rapid sequencing time with results available in hours.	• Shorter read lengths compared to other techniques, typically around 200 base pairs. • Limited accuracy compared to other technologies.
PacBio SMRT sequencing	• Longest read lengths, typically over 10K base pairs. • High accuracy, with error rates less than 1%. • Suitable for applications requiring high accuracy and long read lengths, such as de novo assembly and characterization of epigenetic modifications.	• High cost per base, making it the most expensive option for most applications. • Lower throughput compared to other technologies, with a smaller number of reads generated in a single run.
Oxford Nanopore	• Long read lengths, typically over 10K base pairs. • High accuracy for longer read lengths, with error rates less than 1%. • Portable and flexible, allowing for sequencing in remote locations or in real-time.	• High cost per base compared to other technologies, although lower than PacBio SMRT sequencing. • Lower throughput compared to other technologies, with a smaller number of reads generated in a single run. • Higher variability in accuracy compared to other technologies, with a higher error rate for shorter read lengths.

Technology

Pros

Cons

Illumina sequencing

• Widely used, with a large user base and well-established protocols.

• High-throughput, with the ability to gen erate a large amount of data in a single run.

• Low cost per base, making it the most cost-effective option for many applications.

• Read lengths are shorter compared to other techniques, typically 150–300 base pairs.

• Limited accuracy for longer read lengths and lower accuracy for genomic regions with high GC content.

ThermoFisher’s Ion Torrent

• High-throughput with a large number of reads generated in a single run.

• Lower cost per base compared to other technologies.

• Rapid sequencing time with results available in hours.

• Shorter read lengths compared to other techniques, typically around 200 base pairs.

• Limited accuracy compared to other technologies.

PacBio SMRT sequencing

• Longest read lengths, typically over 10K base pairs.

• High accuracy, with error rates less than 1%.

• Suitable for applications requiring high accuracy and long read lengths, such as de novo assembly and characterization of epigenetic modifications.

• High cost per base, making it the most expensive option for most applications.

• Lower throughput compared to other technologies, with a smaller number of reads generated in a single run.

Oxford Nanopore

• Long read lengths, typically over 10K base pairs.

• High accuracy for longer read lengths, with error rates less than 1%.

• Portable and flexible, allowing for sequencing in remote locations or in real-time.

• High cost per base compared to other technologies, although lower than PacBio SMRT sequencing.

• Lower throughput compared to other technologies, with a smaller number of reads generated in a single run.

• Higher variability in accuracy compared to other technologies, with a higher error rate for shorter read lengths.