Genomics

Basic idea

DNA is copied using ddNTPs, which terminate DNA synthesis. Fragments are separated by size in a capillary.

DNA passes through a nanopore; changes in electrical current identify the bases.

DNA is copied repeatedly in a circular molecule; multiple passes create a highly accurate consensus sequence.

DNA is copied one base at a time using fluorescently labeled nucleotides.

How bases are detected

Fluorescent ddNTPs

Electrical current changes

Fluorescent signals from DNA synthesis

Fluorescence from each incorporated base

Read length

Short (~500–1,000 bp)

Very long (often 10 kb–100+ kb)

Long (~10–25+ kb commonly)

Short (~50–300 bp)

Accuracy

Very high

High, but historically lower than Illumina/PacBio HiFi; improving

Extremely high (~99.9%+)

Extremely high (~99.9%+)

Can sequence long DNA?

❌ No

✅ Excellent

✅ Excellent

❌ No

Amount of DNA needed

Relatively small

Small/moderate

Relatively more DNA and careful preparation

Small/moderate

Speed

Moderate

Very fast / real-time

Moderate

Fast

Amount of data

Low

Very high

High

Very high

Best for

Sequencing a single gene/fragment or checking a specific mutation

Very long DNA, structural variants, genomes, repetitive regions

Highly accurate long reads, genome assembly, structural variants

Large-scale sequencing, whole genomes, RNA-seq, many samples

Main advantage

Simple, reliable, very accurate

Longest reads + real-time sequencing

Long reads + extremely high accuracy

Extremely accurate + lots of data + relatively inexpensive

Main disadvantage

Low throughput and short reads

Error rate can be higher; DNA quality can matter

More expensive/complex; requires high-quality DNA

Short reads make repetitive/complex regions difficult

Typical use

“Did this particular DNA sequence change?”

“What does this very long DNA region look like?”

“Give me the long sequence, but make it extremely accurate.”

“Sequence millions/billions of bases very accurately.”