Genome assembly

Genome assembly refers to the process of taking a large number of short DNA sequence reads and putting them back together to create a representation of the original chromosomes from which the DNA originated. In a shotgun sequencing project, all the DNA from a source (usually a single organism, anything from a bacterium to a mammal) is first fractured into millions of small pieces. These pieces are then "read" by automated sequencing machines, which can read up to 1000 nucleotides or bases at a time. (The four bases are adenine, guanine, cytosine, and thymine, represented as AGCT.) A genome assembly algorithm works by taking all the pieces and aligning them to one another, and detecting all places where two of the short sequences, or reads, overlap. These overlapping reads can be merged together, and the process continues.

Types of Genome Assembly

There are two main types of genome assembly, Whole Genome Assembly (WGA) and De novo assembly. WGA involves aligning short reads to a reference genome and is less computationally intensive. De novo assembly involves assembling the genome from scratch and is more computationally intensive but can provide a more accurate representation of the original genome.

Genome Assembly Algorithms

There are several different algorithms used for genome assembly, such as Overlap-Layout-Consensus (OLC), De Bruijn Graph (DBG) and Greedy algorithm. These algorithms have different strengths and weaknesses and the choice of algorithm can depend on the specific requirements of the genome project.

Challenges in Genome Assembly

Genome assembly can be a challenging process due to the complexity of genomes, which can contain large amounts of repetitive DNA, and the limitations of current sequencing technologies. Errors in the assembly can lead to gaps in the assembled genome and can also lead to misassemblies where sections of the genome are incorrectly assembled.

See Also

• Genome sequencing
• Bioinformatics
• Computational biology

Genome assembly Resources
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