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Contig vs. Scaffold: What's the Difference?

Edited by Aimie Carlson || By Janet White || Published on February 17, 2024
A contig is a set of overlapping DNA segments that together represent a consensus region of DNA, while a scaffold is a higher-order assembly of contigs, linked together into a single sequence, often including gaps.

Key Differences

A contig represents a continuous sequence of DNA formed by assembling overlapping sequences. A scaffold, however, is formed by ordering and orienting contigs, usually with unknown sequences (gaps) between them.
Contigs are assembled based on direct overlaps in genetic sequences, implying a higher confidence in the continuity of the sequence. Scaffolds, while representing longer sequences, may include gaps that are not sequenced, hence less continuous.
In genome mapping, a contig refers to a subset of the genome where the sequence is reliably known. In contrast, a scaffold provides a broader view of the genome layout but includes regions of uncertainty.
Contigs are crucial in accurately reconstructing the DNA sequence in a specific region. Scaffolds extend this by aligning contigs in a probable order, bridging the gaps with estimated sequences or placeholders.
Contigs offer a more detailed and accurate sequence of DNA regions, while scaffolds are used to map larger segments of the genome, offering a broader but less detailed view.

Comparison Chart


Overlapping DNA segments forming a continuous sequence
Assembled contigs linked together, including gaps

Sequence Continuity

Highly continuous with no gaps
Less continuous, may include gaps

Use in Genome Mapping

Represents a reliable subset of genome sequence
Provides a broader view of genome layout

Detail and Accuracy

Higher detail and accuracy in specific regions
Broader view with less detail due to gaps

Role in Sequencing

Crucial for reconstructing specific DNA sequences
Useful for mapping larger segments of the genome

Contig and Scaffold Definitions


A contig is a continuous sequence of DNA formed from overlapping fragments.
The scientists analyzed the contig to understand the gene's structure.


In genomics, a scaffold is a higher-order structure of DNA organization.
The scaffold provided insights into the genome's overall architecture.


Contigs represent overlapping DNA segments assembled together.
After sequencing, the contig provided a complete view of the chromosome section.


A scaffold in genetics refers to the arrangement of contigs with intervening gaps.
Through the scaffold, scientists could hypothesize about the missing DNA sequences.


A contig is a set of aligned DNA sequences.
The contig was used to identify the mutation responsible for the disease.


A scaffold is an assembly of contigs linked to represent a larger DNA sequence.
The scaffold helped in visualizing the arrangement of chromosomes.


In genetics, a contig refers to a continuous and accurate sequence of DNA.
The contig revealed important information about the evolutionary relationships.


Scaffolds include gaps between contigs, representing longer DNA sequences.
The researchers used scaffolds to study the unsequenced regions of the genome.


A contig is a series of overlapping DNA sequences used in genome mapping.
The genome project achieved a significant milestone by completing a large contig.


Scaffolds are used for mapping larger segments of DNA, including estimated sequences.
The genetic map was constructed using various scaffolds across the genome.


(genetics) A set of overlapping DNA segments, derived from a single source of genetic material, from which the complete sequence may be deduced.


A temporary platform, either supported from below or suspended from above, on which workers sit or stand when performing tasks at heights above the ground.


A raised wooden framework or platform.


What is a contig in genetics?

A contig is a continuous sequence of DNA assembled from overlapping fragments.

How is a scaffold different from a contig?

A scaffold is an assembly of contigs linked together, often with gaps, representing a larger DNA sequence.

How are contigs used in DNA sequencing?

They are used to accurately piece together the sequence of specific genomic regions.

Why are scaffolds important in genomics?

Scaffolds provide a broader view of the genome's layout, including unsequenced regions.

What is the purpose of a contig?

Contigs are used to reconstruct a detailed and accurate sequence of a specific DNA region.

Is a contig more accurate than a scaffold?

Yes, a contig offers higher detail and accuracy in sequencing specific DNA regions.

What does a scaffold reveal about the genome?

It reveals the probable arrangement of contigs and indicates the presence of unsequenced regions.

Are scaffolds used to predict the position of genes?

Yes, scaffolds can help predict gene positions, especially in unsequenced regions.

Can a contig have gaps?

No, contigs are continuous sequences without gaps.

How do researchers determine the order of contigs in a scaffold?

Through a combination of sequencing data, bioinformatics analysis, and sometimes genetic markers.

What role do scaffolds play in genome mapping?

Scaffolds help in mapping larger segments of the genome, providing an overall structural framework.

How are gaps in scaffolds addressed in genomics?

Gaps in scaffolds are areas of unknown sequence, often filled in later as sequencing technology advances.

Can a single genome have multiple scaffolds?

Yes, a genome can be divided into multiple scaffolds, each representing different regions.

Are contigs and scaffolds used in human genome projects?

Yes, they are fundamental tools in human genome projects for mapping and sequencing the human genome.

Can contigs link together to form a scaffold?

Yes, scaffolds are essentially formed by linking contigs, sometimes with gaps between them.

Are contigs unique to a specific organism?

Yes, contigs are specific to the organism from which the DNA was sequenced.

What technologies are used to create contigs?

Technologies like DNA sequencing and bioinformatics tools are used to assemble contigs.

How long can a contig be?

Contig lengths vary widely, depending on the sequencing method and the genome's complexity.

Can scaffolds exist without gaps?

Theoretically, but scaffolds typically include gaps due to the current limitations in sequencing technology.

Do scaffolds provide complete genetic information?

Not entirely, as they often include gaps representing unsequenced or uncertain regions.
About Author
Written by
Janet White
Janet White has been an esteemed writer and blogger for Difference Wiki. Holding a Master's degree in Science and Medical Journalism from the prestigious Boston University, she has consistently demonstrated her expertise and passion for her field. When she's not immersed in her work, Janet relishes her time exercising, delving into a good book, and cherishing moments with friends and family.
Edited by
Aimie Carlson
Aimie Carlson, holding a master's degree in English literature, is a fervent English language enthusiast. She lends her writing talents to Difference Wiki, a prominent website that specializes in comparisons, offering readers insightful analyses that both captivate and inform.

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