What is the Difference Between Contig and Scaffold?

The key difference between a contig and a scaffold is that a contig does not have gaps, while a scaffold consists of contigs and gaps. Both contigs and scaffolds are reconstructed nucleotide sequences in whole-genome sequencing projects. Here are the main differences between them:

• Contig: A contig is a continuous stretch of genomic sequence containing A, C, G, and T bases without gaps. Contigs are assembled from a set of sequence fragments and are the shortest assembly components.
• Scaffold: A scaffold is a portion of genomic sequence reconstructed by chaining contigs together using additional information about the relative position and orientation of the contigs in the genome. Scaffolds are composed of contigs and gaps, and they are used to fill in the missing genomic information. In the hierarchical organization of genome assemblies, scaffolds are assembled into chromosomes if there is sufficient mapping information.

There are three main types of scaffolds, based on their placement and orientation within chromosomes:

1. Placed scaffolds: The scaffolds have been placed within a chromosome.
2. Unlocalized scaffolds: Although the chromosome within which the scaffold occurs is known, the scaffold's position or orientation is not known.
3. Unplaced scaffolds: It is not known which chromosome the scaffold belongs to.

In summary, contigs are continuous sequences without gaps, while scaffolds are sequences composed of contigs and gaps, used to fill in missing genomic information and assemble chromosomes in whole-genome sequencing projects.

Comparative Table: Contig vs Scaffold

Contigs and scaffolds are both reconstructed nucleotide sequences in whole-genome sequencing projects. Here is a table summarizing the differences between them:

Contigs are continuous stretches of genomic sequence containing A, C, G, and T bases without gaps. In contrast, scaffolds consist of contigs and gaps, with contigs in a scaffold separated by gaps. Scaffolds are created by chaining contigs together using additional information about the relative position and orientation of the contigs in the genome.