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DNA sequencing is the laboratory technique for determining the exact order of the nucleotides, or bases, in a DNA molecule. That is the National Human Genome Research Institute (NHGRI) definition, and it is the one this guide uses. The questions researchers most often attach to it are which method to use, how accurate the result is, and how long it takes. This page answers each directly and points to the CASRAI guide for the next step in the workflow.
What is DNA sequencing, and what is meant by sequencing of DNA?
Sequencing DNA means reading the order of its four chemical building blocks. NHGRI describes DNA sequencing as “the general laboratory technique for determining the exact sequence of nucleotides, or bases, in a DNA molecule”, and notes that several methods now exist, each with its own characteristics. The Wellcome Sanger Institute’s education site gives the same idea in practical terms: determining the exact order of the four bases in a specific section of DNA. The human genome, for scale, is about 3.2 billion bases long, according to that site.
In a research workflow the phrase covers three steps that the Sanger Institute’s site names: preparing the sample, reading the sequence, and comparing the result with a reference. The same phrase is used whether you read one short stretch of a cloned plasmid or an entire genome. What changes is the method, the amount of data and the quality checks that apply. The phrases “sequencing DNA”, “sequencing of DNA” and “DNA for sequencing” all refer to this one technique.
What is nucleic acid sequencing?
DNA and RNA are both nucleic acids, so “nucleic acid sequencing” is the wider heading under which DNA sequencing sits. The NHGRI definitions quoted in this guide are written for DNA, and DNA is the subject here.
What are the different methods of DNA sequencing?
NHGRI states that there are now several methods, and that developing more is an active area of genomics research. The table lists the approaches that NHGRI and the Wellcome Sanger Institute describe. It does not rank them, because neither source does.
| Approach | What the source says | Source |
|---|---|---|
| Sanger sequencing | Developed in 1977. It was the method used for the first near-complete human genome, published in 2003, a project that took about 13 years. | Wellcome Sanger Institute, yourgenome.org |
| Imaging DNA polymerase as it copies DNA | A newer approach watches DNA polymerase molecules copy DNA with a very fast movie camera and microscope, using a different coloured dye for each base. | NHGRI, DNA Sequencing Fact Sheet |
| Nanopore sequencing | Single DNA strands are threaded through extremely tiny pores in a membrane. | NHGRI, DNA Sequencing Fact Sheet |
For the first row in depth, including how to read a trace and what a core facility needs from you, use the CASRAI Sanger sequencing guide. For a side-by-side of two widely used platform families, see the Illumina vs Nanopore comparison.
How accurate is gene sequencing?
Accuracy is reported per base, as a quality score. The Phred-style score is defined as Q = −10 log10(e), where e is the estimated probability that the base call is wrong. Illumina’s documentation gives the standard reference points:
| Quality score | Estimated chance a base call is wrong | Predicted base-call accuracy |
|---|---|---|
| Q10 | 1 in 10 | 90% |
| Q20 | 1 in 100 | 99% |
| Q30 | 1 in 1,000 | 99.9% |
| Q40 | 1 in 10,000 | 99.99% |
Two cautions apply when quoting these numbers. First, they are predicted accuracy of individual base calls, produced by the instrument software. They are not a guarantee about a variant call or a whole genome. Illumina’s own wording is that at Q30 “virtually all of the reads will be perfect”; treat that as a statement about base calling, not about everything downstream of it. Second, the figures above come from a manufacturer’s documentation about its own platform, so quote them as such. For how the scores are encoded in files and how to filter on them, read the CASRAI guides on Phred quality scores and the FASTQ format.
How long does DNA sequencing take?
There is no single answer, because “how long” mixes three separate clocks. Keep them apart when you plan a project.
- Instrument run time. This is the part that has changed most. The first human genome draft was produced over a 15-month period, from April 1999 to June 2000, and the full Human Genome Project took about 13 years (NHGRI). The Sanger Institute’s education site says current technology can sequence an entire human genome in less than an hour, and that the Institute in 2022 produced a gold-standard human genome every 12 minutes. That is instrument time only.
- Sample and library preparation. The first of the three steps named above happens before the instrument runs and is not included in the run-time figures. Neither NHGRI nor the Sanger Institute gives a duration for it, so plan it from your own protocol or your facility.
- Analysis and queue time. Comparing reads with a reference, quality filtering and any submission to a public archive come after the run, and a shared core facility’s queue sits in front of it. The CASRAI Sanger guide covers core-facility turnaround for that method; for depth and breadth of coverage, see depth vs breadth of coverage.
How the cost of sequencing changed
NHGRI publishes a historical record of sequencing costs, and the milestones show why the timeline above compressed so sharply. These are NHGRI’s dated figures, not current prices for any product.
- The Human Genome Project draft: an estimated cost of about $300 million worldwide.
- The whole project: about $2.7 billion, against a projected US share of $3 billion, finishing in about 13 years rather than the planned 15.
- By 2006: about $14 million for a human genome.
- Mid-2015: just above $4,000. Late 2015: below $1,500, with a whole exome generally below $1,000.
NHGRI’s fact sheet adds that an entire genome can now be sequenced for just a few thousand dollars, and that its stated goal is a high-quality human genome for less than $1,000.
Reading the output: a route map through CASRAI guides
Once the run finishes, which guide you need depends on what came off the instrument.
- A single-read trace from a core facility: Sanger sequencing guide.
- A file of reads with per-base qualities: FASTQ format explained, then Phred quality scores.
- A question about whether you sequenced enough: depth vs breadth of coverage.
- Data ready to deposit: submitting sequence data to NCBI SRA.
Frequently asked questions
What is DNA sequencing?
The laboratory technique for determining the exact order of the nucleotides, or bases, in a DNA molecule (NHGRI).
What are the different methods of DNA sequencing?
NHGRI says there are several, each with its own characteristics, including Sanger sequencing and newer approaches such as imaging DNA polymerase and nanopores. See the methods table above.
How accurate is gene sequencing?
Accuracy is stated per base as a quality score. Illumina’s documentation gives Q30 as a predicted 99.9% base-call accuracy and Q40 as 99.99%. These are predictions for individual base calls, not guarantees for a whole genome.
How long does DNA sequencing take?
It depends on which clock you mean. Instrument time for a human genome is now minutes to hours according to the Sanger Institute’s education site, compared with about 13 years for the Human Genome Project; sample preparation, analysis and facility queues are additional.
What is meant by sequencing of DNA?
Reading the order of the four bases in a stretch of DNA: preparing the sample, reading the sequence and comparing it with a reference.
What is nucleic acid sequencing?
The umbrella term for sequencing DNA or RNA. This guide covers DNA; the NHGRI definitions it quotes are written for DNA.
Sources
- National Human Genome Research Institute, Genetics Glossary: DNA Sequencing, checked 2026-10-29.
- National Human Genome Research Institute, DNA Sequencing Fact Sheet, checked 2026-10-29.
- National Human Genome Research Institute, The Cost of Sequencing a Human Genome, checked 2026-10-29.
- Illumina, Quality scores for next-generation sequencing, checked 2026-10-29.
- Wellcome Sanger Institute, yourgenome: What is DNA sequencing?, checked 2026-10-29.
