So, this is the key difference between contig and scaffold. In contrast, a scaffold is a portion of genomic sequence reconstructed by chaining contigs together. What is the Difference Between Contig and Scaffold?Ī contig is a continuous sequence assembled from a set of sequence fragments. Scaffolds are composed of contigs and gaps.Contig and scaffold are genomic sequences composed of nucleotide sequences.What are the Similarities Between Contig and Scaffold? Moreover, some scaffolds can be filtered out during the assembly. Hence, one chromosome may be represented by several scaffolds. Whole-genome shotgun assembly aims at representing each genomic sequence in one scaffold. Scaffold creation needs information regarding the relative position and orientation of the contigs in the genome. Therefore, scaffolds are created by chaining contigs together and separating them by gaps. Structurally, a scaffold consists of contigs and gaps. What is a Scaffold?Ī scaffold is a reconstructed genomic sequence from end-sequenced whole-genome shotgun clones. Contig assembly typically requires the understanding of algorithms in string matching and sequence alignment. Contigs are assembled finally into a complete genomic sequence. Basically, contig assembly is an important step in whole-genome shotgun sequencing. It requires additional information about the relative position and orientation of the contigs in the genome. Contigs are chained together when creating a scaffold. Contig creation involves the identification of overlapping sequence fragments based on local string matching and alignment methods which identify overlapping ends of the sequences.Ĭontigs do not have gaps. In simple words, contig is an assemblage of a set of sequence fragments. It is formed by putting together several little overlapping bits of DNA into a longer sequence. It is a continuous stretch of sequences composed of A, C, G and T bases.
Side by Side Comparison – Contig vs Scaffold in Tabular FormĬontig is a genomic sequence. Similarities Between Contig and Scaffoldĥ. Both contig and scaffold are reconstructed genomic sequences. Therefore, contig is a continuous stretch of nucleotide sequences while scaffold is a portion of the genome consisting of contigs and gaps. Then the contigs are assembled into scaffolds and finally into a chromosome. In this method, small fragments are assembled into larger fragments and then into larger contigs using a computer. It is a method that sequences many overlapping DNA fragments in parallel. Whole-genome shotgun sequencing is an easy and fast genome sequencing technique for multicellular genomes. Genome sequencing of multicellular organisms is very difficult compared to the sequencing of unicellular organisms. The key difference between contig and scaffold is that a contig does not have gaps while a scaffold consists of contigs and gaps.
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