Glossary: Difference between revisions
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[[File: | [[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. | ||
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== 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. | |||
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== How to use this page == | == How to use this page == | ||
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== Typical applications == | == Typical applications == | ||
* Quick reference for new readers. | * Quick reference for new readers. | ||
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* Support for classroom and laboratory onboarding. | * Support for classroom and laboratory onboarding. | ||
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== | == 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. | |||
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== 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. | |||
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== Related pages == | == Related pages == | ||
* [[Introduction]] | * [[Introduction]] | ||
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* [[Nanopore sequencing]] | * [[Nanopore sequencing]] | ||
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== References == | == References == | ||
* [https://nanoporetech.com/ Oxford Nanopore file formats] | * [https://nanoporetech.com/ Oxford Nanopore file formats] | ||
Latest revision as of 09:24, 15 July 2026
Glossary is part of the Nanopore Wiki learning path. This glossary defines common terms used in nanopore technology, sequencing, signal analysis, and experimental workflows.
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.
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.
How to use this page
| 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. |
Typical applications
- Quick reference for new readers.
- Editorial consistency across translated pages.
- Support for classroom and laboratory onboarding.
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.
Interpretation limits
- Using sequencing terms for non-sequencing nanopore experiments without qualification.
- 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.