Bioinformatics - Revision history

Nano: Expand Nanopore Wiki source page with structured educational content

2026-07-15T01:25:02Z

Expand Nanopore Wiki source page with structured educational content

← Older revision		Revision as of 09:25, 15 July 2026
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	<translate>		<translate>
	<!--T:1-->		<!--T:1-->
	[[File:Nanopore_DNA_sequencing.png\|thumb\|right\|320px\|~~FASTQ stores~~ sequence ~~reads and quality scores. Source: Wikimedia Commons, CC BY 4.0.]]~~		[[File:Nanopore_DNA_sequencing.png\|thumb\|right\|320px\|Nanopore bioinformatics converts raw signal into interpretable sequence evidence.]]
	~~[[File:Oxford_Nanopore_MinION_top_open.jpg\|thumb\|right\|320px\|Sequence alignment is a common downstream bioinformatics task. Source: Wikimedia Commons, CC BY 4.0~~.]]
	'''Bioinformatics''' is part of the Nanopore Wiki learning path. Nanopore bioinformatics converts raw signals and reads into interpretable sequence, alignment, assembly, variant, modification, and classification results.		'''Bioinformatics''' is part of the Nanopore Wiki learning path. Nanopore bioinformatics converts raw signals and reads into interpretable sequence, alignment, assembly, variant, modification, and classification results.

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	<!--T:3-->		<!--T:3-->
			== Scientific basis ==
			* Basecalling converts raw signal into sequence and quality values.
			* Read quality, length distribution, adapters, contamination, and coverage shape downstream results.
			* Interpretations should be tied to measurable quantities, experimental controls, and documented analysis settings.
			* Claims should distinguish direct observations from downstream inference.

			<!--T:4-->
	== Sequencing data workflow ==		== Sequencing data workflow ==
	{\| class="wikitable np-knowledge-table"		{\| class="wikitable np-knowledge-table"
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	\|}		\|}

	<!--T:4-->		<!--T:5-->
	== Typical applications ==		== Typical applications ==
	* Genome assembly.		* Genome assembly.
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	* RNA sequencing and modification detection.		* RNA sequencing and modification detection.

	<!--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.
			* Keep laboratory metadata linked to the raw signal or sequencing run before interpreting results.

			<!--T:7-->
			== Interpretation limits ==
	* Using a pipeline without recording model versions.		* Using a pipeline without recording model versions.
	* Ignoring contamination and coverage bias.		* Ignoring contamination and coverage bias.
	* ~~Overstating clinical~~ or ~~taxonomic conclusions from weak evidence~~.		* 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 ==
	* [[Nanopore sequencing]]		* [[Nanopore sequencing]]
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	* [[Glossary]]		* [[Glossary]]

	<!--T:7-->		<!--T:9-->
	== References ==		== References ==
	* [https://en.wikipedia.org/wiki/Bioinformatics Bioinformatics]		* [https://en.wikipedia.org/wiki/Bioinformatics Bioinformatics]

Nano: Use topic-specific Wikimedia Commons illustrations

2026-07-02T08:50:56Z

Use topic-specific Wikimedia Commons illustrations

← Older revision		Revision as of 16:50, 2 July 2026
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	[[File:Nanopore_DNA_sequencing.png\|thumb\|right\|320px\|FASTQ stores sequence reads and quality scores. Source: Wikimedia Commons, CC BY 4.0.]]		[[File:Nanopore_DNA_sequencing.png\|thumb\|right\|320px\|FASTQ stores sequence reads and quality scores. Source: Wikimedia Commons, CC BY 4.0.]]
	[[File:~~Nanopore_DNA_sequencing~~.~~png~~\|thumb\|right\|320px\|Sequence alignment is a common downstream bioinformatics task. Source: Wikimedia Commons, CC BY 4.0.]]		[[File:Oxford_Nanopore_MinION_top_open.jpg\|thumb\|right\|320px\|Sequence alignment is a common downstream bioinformatics task. Source: Wikimedia Commons, CC BY 4.0.]]
	'''Bioinformatics''' is part of the Nanopore Wiki learning path. Nanopore bioinformatics converts raw signals and reads into interpretable sequence, alignment, assembly, variant, modification, and classification results.		'''Bioinformatics''' is part of the Nanopore Wiki learning path. Nanopore bioinformatics converts raw signals and reads into interpretable sequence, alignment, assembly, variant, modification, and classification results.

Nano: Use topic-specific Wikimedia Commons illustrations

2026-07-02T08:47:24Z

Use topic-specific Wikimedia Commons illustrations

← Older revision		Revision as of 16:47, 2 July 2026
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	[[File:~~Formato-fastq~~.~~svg~~\|thumb\|right\|320px\|FASTQ stores sequence reads and quality scores. Source: Wikimedia Commons, CC BY 4.0.]]		[[File:Nanopore_DNA_sequencing.png\|thumb\|right\|320px\|FASTQ stores sequence reads and quality scores. Source: Wikimedia Commons, CC BY 4.0.]]
	[[File:~~Histone Alignment~~.png\|thumb\|right\|320px\|Sequence alignment is a common downstream bioinformatics task. Source: Wikimedia Commons, CC BY 4.0.]]		[[File:Nanopore_DNA_sequencing.png\|thumb\|right\|320px\|Sequence alignment is a common downstream bioinformatics task. Source: Wikimedia Commons, CC BY 4.0.]]
	'''Bioinformatics''' is part of the Nanopore Wiki learning path. Nanopore bioinformatics converts raw signals and reads into interpretable sequence, alignment, assembly, variant, modification, and classification results.		'''Bioinformatics''' is part of the Nanopore Wiki learning path. Nanopore bioinformatics converts raw signals and reads into interpretable sequence, alignment, assembly, variant, modification, and classification results.

Nano: Restore visible brand name to Nanopore Wiki

2026-06-30T03:47:17Z

Restore visible brand name to Nanopore Wiki

← Older revision		Revision as of 11:47, 30 June 2026
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	[[File:Formato-fastq.svg\|thumb\|right\|320px\|FASTQ stores sequence reads and quality scores. Source: Wikimedia Commons, CC BY 4.0.]]		[[File:Formato-fastq.svg\|thumb\|right\|320px\|FASTQ stores sequence reads and quality scores. Source: Wikimedia Commons, CC BY 4.0.]]
	[[File:Histone Alignment.png\|thumb\|right\|320px\|Sequence alignment is a common downstream bioinformatics task. Source: Wikimedia Commons, CC BY 4.0.]]		[[File:Histone Alignment.png\|thumb\|right\|320px\|Sequence alignment is a common downstream bioinformatics task. Source: Wikimedia Commons, CC BY 4.0.]]
	'''Bioinformatics''' is part of the Wiki learning path. Nanopore bioinformatics converts raw signals and reads into interpretable sequence, alignment, assembly, variant, modification, and classification results.		'''Bioinformatics''' is part of the Nanopore Wiki learning path. Nanopore bioinformatics converts raw signals and reads into interpretable sequence, alignment, assembly, variant, modification, and classification results.

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Nano: Shorten visible site name to Wiki

2026-06-30T03:42:21Z

Shorten visible site name to Wiki

← Older revision		Revision as of 11:42, 30 June 2026
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	[[File:Formato-fastq.svg\|thumb\|right\|320px\|FASTQ stores sequence reads and quality scores. Source: Wikimedia Commons, CC BY 4.0.]]		[[File:Formato-fastq.svg\|thumb\|right\|320px\|FASTQ stores sequence reads and quality scores. Source: Wikimedia Commons, CC BY 4.0.]]
	[[File:Histone Alignment.png\|thumb\|right\|320px\|Sequence alignment is a common downstream bioinformatics task. Source: Wikimedia Commons, CC BY 4.0.]]		[[File:Histone Alignment.png\|thumb\|right\|320px\|Sequence alignment is a common downstream bioinformatics task. Source: Wikimedia Commons, CC BY 4.0.]]
	'''Bioinformatics''' is part of the ~~Nanopore~~ Wiki learning path. Nanopore bioinformatics converts raw signals and reads into interpretable sequence, alignment, assembly, variant, modification, and classification results.		'''Bioinformatics''' is part of the Wiki learning path. Nanopore bioinformatics converts raw signals and reads into interpretable sequence, alignment, assembly, variant, modification, and classification results.

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Nano: Use topic-specific Wikimedia Commons illustrations

2026-06-30T02:56:44Z

Use topic-specific Wikimedia Commons illustrations

← Older revision		Revision as of 10:56, 30 June 2026
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	[[File:~~Nanopore_sequencing_principle~~.png\|thumb\|right\|320px\|~~Nanopore sequencing principle~~. ~~Openly licensed schematic used as a general visual guide~~.]]		[[File:Formato-fastq.svg\|thumb\|right\|320px\|FASTQ stores sequence reads and quality scores. Source: Wikimedia Commons, CC BY 4.0.]]
			[[File:Histone Alignment.png\|thumb\|right\|320px\|Sequence alignment is a common downstream bioinformatics task. Source: Wikimedia Commons, CC BY 4.0.]]
	'''Bioinformatics''' is part of the Nanopore Wiki learning path. Nanopore bioinformatics converts raw signals and reads into interpretable sequence, alignment, assembly, variant, modification, and classification results.		'''Bioinformatics''' is part of the Nanopore Wiki learning path. Nanopore bioinformatics converts raw signals and reads into interpretable sequence, alignment, assembly, variant, modification, and classification results.

Nano: Expand Nanopore Wiki source page with structured educational content

2026-06-30T02:11:59Z

Expand Nanopore Wiki source page with structured educational content

← Older revision		Revision as of 10:11, 30 June 2026
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			__NOTOC__
	<translate>		<translate>
	~~= Bioinformatics =~~ <!--T:1-->		<!--T:1-->
			[[File:Nanopore_sequencing_principle.png\|thumb\|right\|320px\|Nanopore sequencing principle. Openly licensed schematic used as a general visual guide.]]
			'''Bioinformatics''' is part of the Nanopore Wiki learning path. Nanopore bioinformatics converts raw signals and reads into interpretable sequence, alignment, assembly, variant, modification, and classification results.

	<!--T:2-->		<!--T:2-->
	~~'''Bioinformatics''' in nanopore research covers the computational steps that transform~~ raw ~~nanopore signals~~ and reads ~~into interpretable biological or technical results~~.		== Core concepts ==
			* Basecalling converts raw signal into sequence and quality values.
			* Read quality, length distribution, adapters, contamination, and coverage shape downstream results.
			* Long reads support assembly and structural variant discovery but still require quality-aware analysis.
			* Model and software versions are part of the scientific record.

	== ~~Key tasks~~ == <!--T:3-->		<!--T:3-->
			== Sequencing data workflow ==
			{\| class="wikitable np-knowledge-table"
			! Step
			! Description
			\|-
			\| 1
			\| Collect raw signal and run metadata.
			\|-
			\| 2
			\| Basecall into reads and quality scores.
			\|-
			\| 3
			\| Run quality control and filtering.
			\|-
			\| 4
			\| Align, assemble, classify, call variants, or detect modifications according to the question.
			\|-
			\| 5
			\| Report tools, versions, parameters, and reference data.
			\|}

	<!--T:4-->		<!--T:4-->
	* Basecalling raw signal into sequence reads.		== Typical applications ==
	* Quality control and read filtering.		* Genome assembly.
	* ~~Read mapping to reference genomes.~~		* Structural variant detection.
	* De novo genome assembly.		* Metagenomics and pathogen classification.
	* ~~Variant calling and structural~~ variant ~~analysis~~.		* RNA sequencing and modification detection.
	* ~~Taxonomic classification for metagenomics~~ and pathogen ~~detection~~.
	* ~~Methylation~~ and ~~other~~ modification ~~analysis~~.

	~~== Notes for this wiki ==~~ <!--T:5-->		<!--T:5-->
			== Common pitfalls ==
			* Using a pipeline without recording model versions.
			* Ignoring contamination and coverage bias.
			* Overstating clinical or taxonomic conclusions from weak evidence.

	<!--T:6-->		<!--T:6-->
	~~Bioinformatics pages should include tool names, input and output formats, assumptions, common failure modes, and links to reproducible workflows when available.~~		== Related pages ==

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

	~~<!--T:8-->~~
	* [[Nanopore sequencing]]		* [[Nanopore sequencing]]
			* [[Data analysis]]
			* [[Event detection]]
	* [[Glossary]]		* [[Glossary]]

			<!--T:7-->
			== References ==
			* [https://en.wikipedia.org/wiki/Bioinformatics Bioinformatics]
			* [https://en.wikipedia.org/wiki/Sequence_alignment Sequence alignment]
	</translate>		</translate>

	<languages />		<languages />

Nano: Marked this version for translation

2026-06-28T14:38:45Z

Marked this version for translation

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

			<!--T:2-->
	'''Bioinformatics''' in nanopore research covers the computational steps that transform raw nanopore signals and reads into interpretable biological or technical results.		'''Bioinformatics''' in nanopore research covers the computational steps that transform raw nanopore signals and reads into interpretable biological or technical results.

	== Key tasks ==		== Key tasks == <!--T:3-->

			<!--T:4-->
	* Basecalling raw signal into sequence reads.		* Basecalling raw signal into sequence reads.
	* Quality control and read filtering.		* Quality control and read filtering.
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	* Methylation and other modification analysis.		* Methylation and other modification analysis.

	== Notes for this wiki ==		== Notes for this wiki == <!--T:5-->

			<!--T:6-->
	Bioinformatics pages should include tool names, input and output formats, assumptions, common failure modes, and links to reproducible workflows when available.		Bioinformatics pages should include tool names, input and output formats, assumptions, common failure modes, and links to reproducible workflows when available.

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

			<!--T:8-->
	* [[Nanopore sequencing]]		* [[Nanopore sequencing]]
	* [[Glossary]]		* [[Glossary]]

Nano: Convert page to Translate-managed source

2026-06-28T14:38:45Z

Convert page to Translate-managed source

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

	= Bioinformatics =		= Bioinformatics =

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	* [[Nanopore sequencing]]		* [[Nanopore sequencing]]
	* [[Glossary]]		* [[Glossary]]
			</translate>

			<languages />

Nano: Fix language navigation encoding and localized link labels

2026-06-28T13:59:07Z

Fix language navigation encoding and localized link labels

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

	= Bioinformatics =		= Bioinformatics =