Glossary - Revision history

Nano: Expand Nanopore Wiki source page with structured educational content

2026-07-15T01:24:40Z

Expand Nanopore Wiki source page with structured educational content

← Older revision		Revision as of 09:24, 15 July 2026
Line 2:		Line 2:
	<translate>		<translate>
	<!--T:1-->		<!--T:1-->
	[[File:~~Nanopore_sequencing_principle~~.png\|thumb\|right\|320px\|~~Principle of nanopore~~ sequencing~~. Source: Wikimedia Commons, CC BY 4.0~~.]]		[[File:Nanopore_DNA_sequencing.png\|thumb\|right\|320px\|Nanopore sequencing and signal terminology are connected across experiment and analysis.]]
	'''Glossary''' is part of the Nanopore Wiki learning path. This glossary defines common terms used in nanopore technology, sequencing, signal analysis, and experimental workflows.		'''Glossary''' is part of the Nanopore Wiki learning path. This glossary defines common terms used in nanopore technology, sequencing, signal analysis, and experimental workflows.

Line 14:		Line 14:

	<!--T:3-->		<!--T:3-->
			== Scientific basis ==
			* Open-pore current: baseline current through an unoccupied pore.
			* Blockade depth: the magnitude of current reduction or signal shift during an event.
			* Interpretations should be tied to measurable quantities, experimental controls, and documented analysis settings.
			* Claims should distinguish direct observations from downstream inference.

			<!--T:4-->
	== How to use this page ==		== How to use this page ==
	{\| class="wikitable np-knowledge-table"		{\| class="wikitable np-knowledge-table"
Line 29:		Line 36:
	\|}		\|}

	<!--T:4-->		<!--T:5-->
	== Typical applications ==		== Typical applications ==
	* Quick reference for new readers.		* Quick reference for new readers.
Line 35:		Line 42:
	* Support for classroom and laboratory onboarding.		* Support for classroom and laboratory onboarding.

	<!--T:5-->		<!--T:6-->
	== ~~Common pitfalls~~ ==		== Quality checks ==
			* Record platform, pore or flow-cell type, chemistry, voltage or acquisition settings, and software versions.
			* Use negative controls, positive controls, and replicate measurements where the claim depends on specificity.
			* Report limitations such as noise, bias, sample degradation, pore instability, or model-dependent analysis.
			* Use the related pages to move from introductory terms to experimental or computational detail.

			<!--T:7-->
			== Interpretation limits ==
	* Using sequencing terms for non-sequencing nanopore experiments without qualification.		* Using sequencing terms for non-sequencing nanopore experiments without qualification.
	* Translating file formats or instrument names that should remain unchanged.		* Translating file formats or instrument names that should remain unchanged.
			* A single result should not be generalized beyond the sample, protocol, instrument state, and analysis pipeline used.
			* Medical, legal, regulatory, or commercial decisions require domain-specific validation beyond this educational summary.

	<!--T:6-->		<!--T:8-->
	== Related pages ==		== Related pages ==
	* [[Introduction]]		* [[Introduction]]
Line 47:		Line 63:
	* [[Nanopore sequencing]]		* [[Nanopore sequencing]]

	<!--T:7-->		<!--T:9-->
	== References ==		== References ==
	* [https://nanoporetech.com/ Oxford Nanopore file formats]		* [https://nanoporetech.com/ Oxford Nanopore file formats]

Nano: Use topic-specific Wikimedia Commons illustrations

2026-07-02T08:47:25Z

Use topic-specific Wikimedia Commons illustrations

← Older revision		Revision as of 16:47, 2 July 2026
Line 2:		Line 2:
	<translate>		<translate>
	<!--T:1-->		<!--T:1-->
	[[File:~~202001 nanopore sequencing~~.~~svg~~\|thumb\|right\|320px\|Principle of nanopore sequencing. Source: Wikimedia Commons, CC BY 4.0.]]		[[File:Nanopore_sequencing_principle.png\|thumb\|right\|320px\|Principle of nanopore sequencing. Source: Wikimedia Commons, CC BY 4.0.]]
	'''Glossary''' is part of the Nanopore Wiki learning path. This glossary defines common terms used in nanopore technology, sequencing, signal analysis, and experimental workflows.		'''Glossary''' is part of the Nanopore Wiki learning path. This glossary defines common terms used in nanopore technology, sequencing, signal analysis, and experimental workflows.

Nano: Restore visible brand name to Nanopore Wiki

2026-06-30T03:47:19Z

Restore visible brand name to Nanopore Wiki

← Older revision		Revision as of 11:47, 30 June 2026
Line 3:		Line 3:
	<!--T:1-->		<!--T:1-->
	[[File:202001 nanopore sequencing.svg\|thumb\|right\|320px\|Principle of nanopore sequencing. Source: Wikimedia Commons, CC BY 4.0.]]		[[File:202001 nanopore sequencing.svg\|thumb\|right\|320px\|Principle of nanopore sequencing. Source: Wikimedia Commons, CC BY 4.0.]]
	'''Glossary''' is part of the Wiki learning path. This glossary defines common terms used in nanopore technology, sequencing, signal analysis, and experimental workflows.		'''Glossary''' is part of the Nanopore Wiki learning path. This glossary defines common terms used in nanopore technology, sequencing, signal analysis, and experimental workflows.

	<!--T:2-->		<!--T:2-->

Nano: Shorten visible site name to Wiki

2026-06-30T03:42:22Z

Shorten visible site name to Wiki

← Older revision		Revision as of 11:42, 30 June 2026
Line 3:		Line 3:
	<!--T:1-->		<!--T:1-->
	[[File:202001 nanopore sequencing.svg\|thumb\|right\|320px\|Principle of nanopore sequencing. Source: Wikimedia Commons, CC BY 4.0.]]		[[File:202001 nanopore sequencing.svg\|thumb\|right\|320px\|Principle of nanopore sequencing. Source: Wikimedia Commons, CC BY 4.0.]]
	'''Glossary''' is part of the ~~Nanopore~~ Wiki learning path. This glossary defines common terms used in nanopore technology, sequencing, signal analysis, and experimental workflows.		'''Glossary''' is part of the Wiki learning path. This glossary defines common terms used in nanopore technology, sequencing, signal analysis, and experimental workflows.

	<!--T:2-->		<!--T:2-->

Nano: Use topic-specific Wikimedia Commons illustrations

2026-06-30T02:56:45Z

Use topic-specific Wikimedia Commons illustrations

← Older revision		Revision as of 10:56, 30 June 2026
Line 2:		Line 2:
	<translate>		<translate>
	<!--T:1-->		<!--T:1-->
	[[File:~~Nanopore_sequencing_principle~~.~~png~~\|thumb\|right\|320px\|~~Nanopore~~ sequencing ~~principle~~. ~~Openly licensed schematic used as a general visual guide~~.]]		[[File:202001 nanopore sequencing.svg\|thumb\|right\|320px\|Principle of nanopore sequencing. Source: Wikimedia Commons, CC BY 4.0.]]
	'''Glossary''' is part of the Nanopore Wiki learning path. This glossary defines common terms used in nanopore technology, sequencing, signal analysis, and experimental workflows.		'''Glossary''' is part of the Nanopore Wiki learning path. This glossary defines common terms used in nanopore technology, sequencing, signal analysis, and experimental workflows.

Nano: Expand Nanopore Wiki source page with structured educational content

2026-06-30T02:10:05Z

Expand Nanopore Wiki source page with structured educational content

← Older revision		Revision as of 10:10, 30 June 2026
Line 1:		Line 1:
			__NOTOC__
	<translate>		<translate>
	~~= Glossary =~~ <!--T:1-->		<!--T:1-->
			[[File:Nanopore_sequencing_principle.png\|thumb\|right\|320px\|Nanopore sequencing principle. Openly licensed schematic used as a general visual guide.]]
			'''Glossary''' is part of the Nanopore Wiki learning path. This glossary defines common terms used in nanopore technology, sequencing, signal analysis, and experimental workflows.

	<!--T:2-->		<!--T:2-->
	~~This glossary collects short definitions used across~~ Nanopore ~~Wiki~~.		== Core concepts ==
			* Open-pore current: baseline current through an unoccupied pore.
			* Blockade depth: the magnitude of current reduction or signal shift during an event.
			* Dwell time: the duration for which a molecule produces a detectable event.
			* Basecalling: conversion of nanopore raw signal into nucleotide sequence and quality values.
			* POD5, FAST5, FASTQ, and BAM: common file formats in Oxford Nanopore workflows.

	<!--T:3-->		<!--T:3-->
	~~; Basecalling~~		== How to use this page ==
	~~: Converting nanopore signal data into nucleotide sequence reads~~.		{\| class="wikitable np-knowledge-table"
			! Step
			! Description
			\|-
			\| 1
			\| Use definitions to keep wording consistent across pages.
			\|-
			\| 2
			\| Prefer exact terms such as open-pore current, blockade event, and Q score.
			\|-
			\| 3
			\| When a term has platform-specific meaning, state the platform explicitly.
			\|}

	<!--T:4-->		<!--T:4-->
	~~; Long read~~		== Typical applications ==
	~~: A sequencing read that is much longer than typical short-read sequencing output, often useful~~ for ~~assembly~~ and ~~structural variant detection~~.		* Quick reference for new readers.
			* Editorial consistency across translated pages.
			* Support for classroom and laboratory onboarding.

	<!--T:5-->		<!--T:5-->
	~~; Nanopore~~		== Common pitfalls ==
	~~: A nanoscale pore used to sense molecules through changes in current, ion flow,~~ or ~~other measurable signals~~.		* Using sequencing terms for non-sequencing nanopore experiments without qualification.
			* Translating file formats or instrument names that should remain unchanged.

	<!--T:6-->		<!--T:6-->
	~~; Read mapping~~		== Related pages ==
	~~: Aligning~~ sequencing ~~reads to a reference genome or reference sequence.~~		* [[Introduction]]
			* [[Bioinformatics]]
			* [[Data analysis]]
			* [[Nanopore sequencing]]

	<!--T:7-->		<!--T:7-->
	~~; Single-molecule sensing~~		== References ==
	: ~~Detecting or measuring individual molecules rather than only bulk averages~~.		* [https://nanoporetech.com/ Oxford Nanopore file formats]
			* [https://en.wikipedia.org/wiki/FASTQ_format FASTQ format]
	~~<!--T~~:~~8-->~~
	~~; Structural variant~~
	~~: A genomic change such as an insertion, deletion, duplication, inversion, or translocation that affects a larger DNA segment~~.
	</translate>		</translate>

	<languages />		<languages />

Nano: Marked this version for translation

2026-06-28T14:38:47Z

Marked this version for translation

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

			<!--T:2-->
	This glossary collects short definitions used across Nanopore Wiki.		This glossary collects short definitions used across Nanopore Wiki.

			<!--T:3-->
	; Basecalling		; Basecalling
	: Converting nanopore signal data into nucleotide sequence reads.		: Converting nanopore signal data into nucleotide sequence reads.

			<!--T:4-->
	; Long read		; Long read
	: A sequencing read that is much longer than typical short-read sequencing output, often useful for assembly and structural variant detection.		: A sequencing read that is much longer than typical short-read sequencing output, often useful for assembly and structural variant detection.

			<!--T:5-->
	; Nanopore		; Nanopore
	: A nanoscale pore used to sense molecules through changes in current, ion flow, or other measurable signals.		: A nanoscale pore used to sense molecules through changes in current, ion flow, or other measurable signals.

			<!--T:6-->
	; Read mapping		; Read mapping
	: Aligning sequencing reads to a reference genome or reference sequence.		: Aligning sequencing reads to a reference genome or reference sequence.

			<!--T:7-->
	; Single-molecule sensing		; Single-molecule sensing
	: Detecting or measuring individual molecules rather than only bulk averages.		: Detecting or measuring individual molecules rather than only bulk averages.

			<!--T:8-->
	; Structural variant		; Structural variant
	: A genomic change such as an insertion, deletion, duplication, inversion, or translocation that affects a larger DNA segment.		: A genomic change such as an insertion, deletion, duplication, inversion, or translocation that affects a larger DNA segment.

Nano: Convert page to Translate-managed source

2026-06-28T14:38:47Z

Convert page to Translate-managed source

← Older revision		Revision as of 22:38, 28 June 2026
Line 1:		Line 1:
	<~~div class="plainlinks"~~>~~'''Languages:''' [[Glossary\|English]] \| [[Glossary/zh\|中文]] \| [[Glossary/es\|español]] \| [[Glossary/fr\|français]] \| [[Glossary/de\|Deutsch]] \| [[Glossary/ja\|日本語]]</div>~~		<translate>

	= Glossary =		= Glossary =

Line 22:		Line 21:
	; Structural variant		; Structural variant
	: A genomic change such as an insertion, deletion, duplication, inversion, or translocation that affects a larger DNA segment.		: A genomic change such as an insertion, deletion, duplication, inversion, or translocation that affects a larger DNA segment.
			</translate>

			<languages />

Nano: Fix language navigation encoding and localized link labels

2026-06-28T13:59:12Z

Fix language navigation encoding and localized link labels

← Older revision		Revision as of 21:59, 28 June 2026
Line 1:		Line 1:
	<div class="plainlinks">'''Languages:''' [[Glossary\|English]] \| [[Glossary/zh\|??]] \| [[Glossary/es\|~~espa?ol~~]] \| [[Glossary/fr\|~~fran?ais~~]] \| [[Glossary/de\|Deutsch]] \| [[Glossary/ja\|~~???~~]]</div>		<div class="plainlinks">'''Languages:''' [[Glossary\|English]] \| [[Glossary/zh\|中文]] \| [[Glossary/es\|español]] \| [[Glossary/fr\|français]] \| [[Glossary/de\|Deutsch]] \| [[Glossary/ja\|日本語]]</div>

	= Glossary =		= Glossary =

Nano: Add language navigation

2026-06-28T13:52:20Z

Add language navigation

← Older revision		Revision as of 21:52, 28 June 2026
Line 1:		Line 1:
			<div class="plainlinks">'''Languages:''' [[Glossary\|English]] \| [[Glossary/zh\|??]] \| [[Glossary/es\|espa?ol]] \| [[Glossary/fr\|fran?ais]] \| [[Glossary/de\|Deutsch]] \| [[Glossary/ja\|???]]</div>

	= Glossary =		= Glossary =