Nanopore sequencing - Revision history

Nano: Marked this version for translation

2026-07-14T13:26:34Z

Marked this version for translation

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	__NOTOC__		__NOTOC__
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	= Nanopore sequencing =		= Nanopore sequencing =
	~~<!--T:1-->~~
	[[File:Nanopore_DNA_sequencing.png\|thumb\|right\|320px\|A DNA molecule passing through a nanopore can produce a signal that is interpreted as sequence information. Source: Wikimedia Commons, CC BY 4.0.]]		[[File:Nanopore_DNA_sequencing.png\|thumb\|right\|320px\|A DNA molecule passing through a nanopore can produce a signal that is interpreted as sequence information. Source: Wikimedia Commons, CC BY 4.0.]]
	'''Nanopore sequencing''' is a single-molecule sequencing approach in which DNA or RNA molecules pass through nanopores and produce signal changes that are computationally converted into sequence information. In practical systems, a motor protein controls molecular movement, many pores operate in parallel, and neural-network basecallers translate raw signal into reads.		'''Nanopore sequencing''' is a single-molecule sequencing approach in which DNA or RNA molecules pass through nanopores and produce signal changes that are computationally converted into sequence information. In practical systems, a motor protein controls molecular movement, many pores operate in parallel, and neural-network basecallers translate raw signal into reads.
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	The scientific value of nanopore sequencing comes from four connected properties: long reads, real-time acquisition, direct electrical sensing, and portable instrumentation. These properties make it useful for genome assembly, structural-variant analysis, microbial surveillance, outbreak response, environmental sequencing, transcriptomics, and direct detection of some nucleotide modifications.		The scientific value of nanopore sequencing comes from four connected properties: long reads, real-time acquisition, direct electrical sensing, and portable instrumentation. These properties make it useful for genome assembly, structural-variant analysis, microbial surveillance, outbreak response, environmental sequencing, transcriptomics, and direct detection of some nucleotide modifications.

			<!--T:3-->
	== Principle ==		== Principle ==
	~~<!--T:3-->~~
	A nanopore sequencing measurement has three coupled layers:		A nanopore sequencing measurement has three coupled layers:
	* '''Molecular layer''' - a DNA or RNA strand is prepared with adapters and is guided through a pore by an enzyme or motor protein.		* '''Molecular layer''' - a DNA or RNA strand is prepared with adapters and is guided through a pore by an enzyme or motor protein.
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	A single current level is usually not assigned to one isolated base. The measured signal depends on a local sequence context, pore chemistry, motor speed, temperature, buffer, electronics, and model version. This is why basecalling and modified-base detection are model-based tasks rather than simple lookup tables.		A single current level is usually not assigned to one isolated base. The measured signal depends on a local sequence context, pore chemistry, motor speed, temperature, buffer, electronics, and model version. This is why basecalling and modified-base detection are model-based tasks rather than simple lookup tables.

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	== Workflow from sample to result ==		== Workflow from sample to result ==
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	{\| class="wikitable np-knowledge-table"		{\| class="wikitable np-knowledge-table"
	! Stage !! Main question !! Typical output !! Quality checks		! Stage !! Main question !! Typical output !! Quality checks
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	\|}		\|}

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	== Strengths ==		== Strengths ==
	~~<!--T:6-->~~
	* '''Long reads''' can span repeats, structural variants, haplotypes, plasmids, and complex genomic regions.		* '''Long reads''' can span repeats, structural variants, haplotypes, plasmids, and complex genomic regions.
	* '''Real-time sequencing''' allows analysis during a run and supports rapid decision-making.		* '''Real-time sequencing''' allows analysis during a run and supports rapid decision-making.
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	* '''Flexible throughput''' allows small targeted runs and larger genome-scale projects.		* '''Flexible throughput''' allows small targeted runs and larger genome-scale projects.

			<!--T:7-->
	== Limitations and error sources ==		== Limitations and error sources ==
	~~<!--T:7-->~~
	Nanopore sequencing should not be treated as automatically superior to short-read sequencing. Its suitability depends on the question, sample, required accuracy, cost, and analysis pipeline. Important limitations include:		Nanopore sequencing should not be treated as automatically superior to short-read sequencing. Its suitability depends on the question, sample, required accuracy, cost, and analysis pipeline. Important limitations include:
	* Raw read errors and systematic context-dependent errors.		* Raw read errors and systematic context-dependent errors.
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	* Need for careful controls in clinical, regulatory, or high-consequence settings.		* Need for careful controls in clinical, regulatory, or high-consequence settings.

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	== Applications ==		== Applications ==
	~~<!--T:8-->~~
	* '''Genome assembly''' - long reads help resolve repeats and structural complexity.		* '''Genome assembly''' - long reads help resolve repeats and structural complexity.
	* '''Structural variation''' - long reads can span insertions, deletions, inversions, translocations, and repeat expansions.		* '''Structural variation''' - long reads can span insertions, deletions, inversions, translocations, and repeat expansions.
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	* '''Adaptive sampling''' - real-time enrichment or depletion of targets by deciding whether to continue sequencing a molecule.		* '''Adaptive sampling''' - real-time enrichment or depletion of targets by deciding whether to continue sequencing a molecule.

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	== Data and file types ==		== Data and file types ==
	~~<!--T:9-->~~
	Raw and processed nanopore data may include POD5 or FAST5 signal files, FASTQ reads, BAM or CRAM alignments, sequencing-summary files, modified-base tags, and run reports. Good analysis practice records the instrument, flow cell, chemistry, kit, basecaller, model version, reference database, and command-line parameters.		Raw and processed nanopore data may include POD5 or FAST5 signal files, FASTQ reads, BAM or CRAM alignments, sequencing-summary files, modified-base tags, and run reports. Good analysis practice records the instrument, flow cell, chemistry, kit, basecaller, model version, reference database, and command-line parameters.

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	== Good practice ==		== Good practice ==
	~~<!--T:10-->~~
	* Match the protocol to the biological question before optimizing yield.		* Match the protocol to the biological question before optimizing yield.
	* Use controls to separate library, pore, sample, and analysis effects.		* Use controls to separate library, pore, sample, and analysis effects.
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	* Validate high-impact conclusions with independent evidence when possible.		* Validate high-impact conclusions with independent evidence when possible.

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	== Selected papers and resources ==		== Selected papers and resources ==
	~~<!--T:11-->~~
	* Deamer D, Akeson M, Branton D. [https://www.nature.com/articles/nbt.3423 Three decades of nanopore sequencing]. ''Nature Biotechnology''. 2016.		* Deamer D, Akeson M, Branton D. [https://www.nature.com/articles/nbt.3423 Three decades of nanopore sequencing]. ''Nature Biotechnology''. 2016.
	* Jain M et al. [https://www.nature.com/articles/nbt.4060 Nanopore sequencing and assembly of a human genome with ultra-long reads]. ''Nature Biotechnology''. 2018.		* Jain M et al. [https://www.nature.com/articles/nbt.4060 Nanopore sequencing and assembly of a human genome with ultra-long reads]. ''Nature Biotechnology''. 2018.
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	* Oxford Nanopore Technologies. [https://github.com/nanoporetech/dorado Dorado basecaller and related tools].		* Oxford Nanopore Technologies. [https://github.com/nanoporetech/dorado Dorado basecaller and related tools].

			<!--T:12-->
	== Related pages ==		== Related pages ==
	~~<!--T:12-->~~
	* [[Nanopore technology]]		* [[Nanopore technology]]
	* [[Oxford Nanopore]]		* [[Oxford Nanopore]]

Nano: Deepen scientific structure of nanopore sequencing page

2026-07-14T13:26:28Z

Deepen scientific structure of nanopore sequencing page

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-= Nanopore sequencing = <!--T:1-->
+= Nanopore sequencing =
 <!--T:2-->
-'''Nanopore sequencing''' is a sequencing approach in which individual DNA or RNA molecules pass through nanopores and produce signal changes that can be interpreted as sequence information.
+The scientific value of nanopore sequencing comes from four connected properties: long reads, real-time acquisition, direct electrical sensing, and portable instrumentation. These properties make it useful for genome assembly, structural-variant analysis, microbial surveillance, outbreak response, environmental sequencing, transcriptomics, and direct detection of some nucleotide modifications.
-== Features == <!--T:3-->
+== Principle ==
 <!--T:4-->
-* Long reads that can help with genome assembly and structural variant detection.
+A single current level is usually not assigned to one isolated base. The measured signal depends on a local sequence context, pore chemistry, motor speed, temperature, buffer, electronics, and model version. This is why basecalling and modified-base detection are model-based tasks rather than simple lookup tables.
-== Common workflow == <!--T:5-->
+== Workflow from sample to result ==
 <!--T:6-->
-# Sample preparation and library construction.
+* '''Long reads''' can span repeats, structural variants, haplotypes, plasmids, and complex genomic regions.
-# Sequencing on a nanopore device.
+* '''Real-time sequencing''' allows analysis during a run and supports rapid decision-making.
-# Basecalling from raw signal to nucleotide sequence.
+* '''Direct sensing''' can preserve information about some DNA or RNA modifications.
-# Quality control and filtering.
+* '''Portable instruments''' make field, teaching, and low-infrastructure workflows possible.
-# Alignment, assembly, variant calling, or metagenomic classification.
+* '''Flexible throughput''' allows small targeted runs and larger genome-scale projects.
-== Related pages == <!--T:7-->
+== Limitations and error sources ==
 <!--T:8-->
 * [[Oxford Nanopore]]
 * [[MinION]]
 * [[Bioinformatics]]
 * [[Glossary]]
 </translate>
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Nano: Marked this version for translation

2026-06-28T14:38:41Z

Marked this version for translation

← Older revision		Revision as of 22:38, 28 June 2026
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	= Nanopore sequencing =		= Nanopore sequencing = <!--T:1-->

			<!--T:2-->
	'''Nanopore sequencing''' is a sequencing approach in which individual DNA or RNA molecules pass through nanopores and produce signal changes that can be interpreted as sequence information.		'''Nanopore sequencing''' is a sequencing approach in which individual DNA or RNA molecules pass through nanopores and produce signal changes that can be interpreted as sequence information.

	== Features ==		== Features == <!--T:3-->

			<!--T:4-->
	* Long reads that can help with genome assembly and structural variant detection.		* Long reads that can help with genome assembly and structural variant detection.
	* Real-time data generation and analysis.		* Real-time data generation and analysis.
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	* Portable instruments suitable for field and rapid-response settings.		* Portable instruments suitable for field and rapid-response settings.

	== Common workflow ==		== Common workflow == <!--T:5-->

			<!--T:6-->
	# Sample preparation and library construction.		# Sample preparation and library construction.
	# Sequencing on a nanopore device.		# Sequencing on a nanopore device.
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	# Interpretation and reporting.		# Interpretation and reporting.

	== Related pages ==		== Related pages == <!--T:7-->

			<!--T:8-->
	* [[Oxford Nanopore]]		* [[Oxford Nanopore]]
	* [[MinION]]		* [[MinION]]

Nano: Convert page to Translate-managed source

2026-06-28T14:38:41Z

Convert page to Translate-managed source

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	<~~div class="plainlinks"~~>'''Languages:''' [[Nanopore sequencing\|English]] \| [[Nanopore sequencing/zh\|中文]] \| [[Nanopore sequencing/es\|español]] \| [[Nanopore sequencing/fr\|français]] \| [[Nanopore sequencing/de\|Deutsch]] \| [[Nanopore sequencing/ja\|日本語]]</div>		<translate>

	= Nanopore sequencing =		= Nanopore sequencing =

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	* [[Bioinformatics]]		* [[Bioinformatics]]
	* [[Glossary]]		* [[Glossary]]
			</translate>

			<languages />

Nano: Fix language navigation encoding and localized link labels

2026-06-28T13:58:56Z

Fix language navigation encoding and localized link labels

← Older revision		Revision as of 21:58, 28 June 2026
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	<div class="plainlinks">'''Languages:''' [[Nanopore sequencing\|English]] \| [[Nanopore sequencing/zh\|??]] \| [[Nanopore sequencing/es\|~~espa?ol~~]] \| [[Nanopore sequencing/fr\|~~fran?ais~~]] \| [[Nanopore sequencing/de\|Deutsch]] \| [[Nanopore sequencing/ja\|~~???~~]]</div>		<div class="plainlinks">'''Languages:''' [[Nanopore sequencing\|English]] \| [[Nanopore sequencing/zh\|中文]] \| [[Nanopore sequencing/es\|español]] \| [[Nanopore sequencing/fr\|français]] \| [[Nanopore sequencing/de\|Deutsch]] \| [[Nanopore sequencing/ja\|日本語]]</div>

	= Nanopore sequencing =		= Nanopore sequencing =

Nano: Add language navigation

2026-06-28T13:49:20Z

Add language navigation

← Older revision		Revision as of 21:49, 28 June 2026
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			<div class="plainlinks">'''Languages:''' [[Nanopore sequencing\|English]] \| [[Nanopore sequencing/zh\|??]] \| [[Nanopore sequencing/es\|espa?ol]] \| [[Nanopore sequencing/fr\|fran?ais]] \| [[Nanopore sequencing/de\|Deutsch]] \| [[Nanopore sequencing/ja\|???]]</div>

	= Nanopore sequencing =		= Nanopore sequencing =

Nano: Create core Nanopore Wiki topic page

2026-06-28T12:38:01Z

Create core Nanopore Wiki topic page

New page

= Nanopore sequencing =

'''Nanopore sequencing''' is a sequencing approach in which individual DNA or RNA molecules pass through nanopores and produce signal changes that can be interpreted as sequence information.

== Features ==

* Long reads that can help with genome assembly and structural variant detection.
* Real-time data generation and analysis.
* Direct DNA or RNA sensing in many workflows.
* Portable instruments suitable for field and rapid-response settings.

== Common workflow ==

# Sample preparation and library construction.
# Sequencing on a nanopore device.
# Basecalling from raw signal to nucleotide sequence.
# Quality control and filtering.
# Alignment, assembly, variant calling, or metagenomic classification.
# Interpretation and reporting.

== Related pages ==

* [[Oxford Nanopore]]
* [[MinION]]
* [[Bioinformatics]]
* [[Glossary]]