Nanopore Sequencing Glossary
This glossary provides definitions of key terms related to Nanopore sequencing, offering educators and first-time users a foundational understanding of the technology and its associated concepts.
A
Adapter
Short DNA or RNA sequences ligated to sample fragments to facilitate their attachment to sequencing platforms.
Alignment
The process of arranging sequences to identify regions of similarity, which may indicate functional, structural, or evolutionary relationships.
Amplicon
A DNA fragment that has been amplified by PCR.
B
Base Modification
Chemical alterations to DNA bases, such as methylation, which can affect gene expression.
Basecalling
The process of determining the sequence of nucleotides (bases) from raw signal data generated by the sequencing platform.
Barcode
Short, unique sequences added to DNA fragments to identify and differentiate multiple samples sequenced together. See also Indexing.
C
Chimera
A sequence artifact formed by the joining of two or more unrelated DNA fragments.
Consensus Sequence
A sequence derived from the alignment of multiple sequences, representing the most common nucleotide at each position.
Contig
A contiguous sequence assembled from overlapping reads.
Coverage
The number of times a nucleotide is read during sequencing; higher coverage increases confidence in the accuracy of the sequence.
D
De Novo Sequencing
Sequencing a novel genome without a reference, assembling the sequence from scratch.
Demultiplexing
The process of sorting sequences from a mixed sample pool into individual datasets based on their barcodes.
Direct RNA Sequencing
Sequencing RNA molecules directly without converting them to cDNA, preserving base modifications.
DNA Library
A collection of DNA fragments prepared for sequencing.
Dorado
A basecalling software developed by Oxford Nanopore Technologies for translating raw nanopore signals into nucleotide sequences.
E
Epigenetics
The study of heritable changes in gene expression that do not involve changes to the underlying DNA sequence.
Epigenome
The complete set of epigenetic modifications on the genetic material of a cell.
F
FAST5
A file format previously used by ONT to store raw signal data from nanopore sequencing. It has been replaced by POD5.
FASTQ
A common file format for storing nucleotide sequences and associated quality scores.
Flow Cell
A consumable device containing nanopores through which nucleic acids pass during sequencing.
G
H
High Molecular Weight (HMW) DNA
Long DNA fragments essential for obtaining long reads in sequencing.
I
Indexing
The use of unique sequences (indexes), also called barcodes, to tag DNA fragments from different samples, enabling their identification after pooled sequencing.
L
Library Preparation
The process of preparing DNA or RNA samples for sequencing, including fragmentation, adapter ligation, and amplification.
Ligation
The enzymatic process of joining two DNA fragments together.
Long Reads
Sequences that are typically longer than 10,000 base pairs, advantageous for resolving repetitive regions and structural variants.
M
MinION
A portable nanopore sequencing device developed by Oxford Nanopore Technologies.
Rapid library preparation kits
Multiplexing
Sequencing multiple samples simultaneously by using unique barcodes for each sample.
N
Nanopore
A nanometer-scale pore used in sequencing to detect changes in ionic current as nucleic acids pass through, allowing base identification.
Native library preparation kits A library preparation kit that uses ligation to attach sequencing adapters; is longer and uses additional 3rd party reagents compared to the rapid library preparation kits but also results in longer fragment lengths.
Oxford Nanopore Technologies (ONT)
The company that developed and commercialized nanopore sequencing technology.
P
Pore
A tiny opening in a membrane through which molecules can pass.
POD5
The current file format used by ONT to store raw sequencing signal data.
PromethION
A high-throughput nanopore sequencing device designed for large-scale projects.
Q
Quality Score (Phred Score)
A metric that indicates the confidence of a base call; higher scores represent greater confidence.
R
Rapid Adapter
Short DNA sequence ligated to sample fragments to facilitate their translocation through the nanopore.
Rapid library preparation kits A library preparation kit that uses a transposase complex to attach sequencing adapters; is quicker and uses fewer 3rd party reagents than the native library preparation kit but also sheers the DNA resulting in smaller fragment lengths.
Read
A sequence of nucleotides generated by a sequencing machine from a single DNA or RNA fragment.
Real-Time Sequencing
The ability to analyze sequencing data as it is generated, enabling immediate insights.
Reference Genome
A representative example of a species' genome used as a standard for comparison.
S
Single Molecule Sequencing
Sequencing technologies that read individual DNA or RNA molecules without amplification.
T
Throughput
The amount of data generated by a sequencing platform in a given time frame.
Translocation
The movement of nucleic acid molecules through a nanopore during sequencing.
U
Ultra-Long Reads
Sequences exceeding 100,000 base pairs, useful for assembling complex genomes.
V
Variant Calling
The process of identifying variations (e.g., SNPs, insertions, deletions) between sequences and a reference genome.
Y
Yield
The total amount of data (in bases) produced by a sequencing run.
Z
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