Bioinformatics: Difference between revisions

Revision as of 10:11, 30 June 2026

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.

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.

Sequencing data workflow

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.

Typical applications

Genome assembly.
Structural variant detection.
Metagenomics and pathogen classification.
RNA sequencing and modification detection.

Common pitfalls

Using a pipeline without recording model versions.
Ignoring contamination and coverage bias.
Overstating clinical or taxonomic conclusions from weak evidence.

@@ Line 1: / Line 1: @@
+__NOTOC__
 <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-->
-'''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-->
-* 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-->
-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]]
+* [[Data analysis]]
+* [[Event detection]]
 * [[Glossary]]
+<!--T:7-->
+== References ==
+* [https://en.wikipedia.org/wiki/Bioinformatics Bioinformatics]
+* [https://en.wikipedia.org/wiki/Sequence_alignment Sequence alignment]
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