Genome assembly

Genome assembly reconstructs long DNA sequences from shorter sequencing reads by identifying overlaps or shared sequence patterns. It produces contiguous sequences that approximate chromosomes or other genomic molecules.

Overlap–layout–consensus: A genome-assembly strategy that builds read overlaps, arranges reads into paths, and derives a consensus sequence. This classic strategy assembles long reads by making their pairwise overlaps explicit.
DNA sequencing: The experimental determination of the nucleotide order in DNA molecules. Sequencing supplies the reads from which an assembly is reconstructed.
De novo genome assembly: Genome reconstruction performed without using a reference genome to guide sequence placement. It is the assembly mode that relies on read evidence rather than a coordinate template.
Genome annotation: The identification and description of genes and other functional elements in a genome sequence. Annotation depends on assembled sequence continuity to locate genomic features.
Repetitive DNA: DNA sequences that occur in multiple copies within a genome. Nearly identical repeats can make the correct placement and copy number ambiguous.
De Bruijn graph: A graph whose vertices represent sequences of length k−1 and whose edges represent sequences of length k. Short-read assemblers use these graphs to reconstruct sequences from shared k-mers.
Sequencing read: A nucleotide sequence recorded from one DNA fragment during a sequencing run. Reads are the basic observations that assemblers compare and combine.
Reference-guided assembly: Genome reconstruction that aligns sequencing reads to an existing reference sequence. It contrasts with de novo assembly by using a prior genome to place reads.
Structural variation: Large genomic differences such as insertions, deletions, inversions, and duplications. Accurate assemblies can reveal rearrangements that short-read mapping may miss.
Genome completeness: The extent to which an assembled genome represents the biological genome being studied. Missing regions can remain undetected even when an assembly appears contiguous.

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