Glossary: Difference between revisions

Revision as of 10:10, 30 June 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.

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.

Common pitfalls

Using sequencing terms for non-sequencing nanopore experiments without qualification.
Translating file formats or instrument names that should remain unchanged.

@@ Line 1: / Line 1: @@
+__NOTOC__
 <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-->
-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
+== 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-->
-; 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-->
-; 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-->
-; Read mapping
+== Related pages ==
-: Aligning sequencing reads to a reference genome or reference sequence.
+* [[Introduction]]
+* [[Bioinformatics]]
+* [[Data analysis]]
+* [[Nanopore sequencing]]
 <!--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.
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