Glossary: Difference between revisions

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.

@@ Line 1: / Line 1: @@
+__NOTOC__
 <translate>
-= Glossary = <!--T:1-->
+<!--T:1-->
+[[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.
 <!--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-->
-; Basecalling
+== Scientific basis ==
-: Converting nanopore signal data into nucleotide sequence reads.
+* 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-->
-; Long read
+== How to use this page ==
-: A sequencing read that is much longer than typical short-read sequencing output, often useful for assembly and structural variant detection.
+{| 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:5-->
-; Nanopore
+== Typical applications ==
-: A nanoscale pore used to sense molecules through changes in current, ion flow, or other measurable signals.
+* Quick reference for new readers.
+* Editorial consistency across translated pages.
+* Support for classroom and laboratory onboarding.
 <!--T:6-->
-; Read mapping
+== Quality checks ==
-: Aligning sequencing reads to a reference genome or reference sequence.
+* 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-->
-; Single-molecule sensing
+== Interpretation limits ==
-: Detecting or measuring individual molecules rather than only bulk averages.
+* 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.
 <!--T:8-->
-; Structural variant
+== Related pages ==
-: A genomic change such as an insertion, deletion, duplication, inversion, or translocation that affects a larger DNA segment.
+* [[Introduction]]
+* [[Bioinformatics]]
+* [[Data analysis]]
+* [[Nanopore sequencing]]
+<!--T:9-->
+== References ==
+* [https://nanoporetech.com/ Oxford Nanopore file formats]
+* [https://en.wikipedia.org/wiki/FASTQ_format FASTQ format]
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