Genome assembly is the process of reconstructing the full DNA sequence of an organism from many shorter fragments generated by sequencing technologies. It is central to modern genomics because most platforms cannot read entire chromosomes in a single pass.

Two major data types drive current assemblies. Short reads are highly accurate but only a few hundred bases long, which complicates reconstruction in repetitive regions. Long reads can span thousands to millions of bases, helping to bridge repeats and structural variants, but they usually have higher per base error rates. Modern projects often combine both, using long reads to build the backbone and short reads for polishing.

Assembly typically begins with read preprocessing and error correction, followed by graph based reconstruction. Overlaps or shared subsequences between reads are used to build contigs, which are contiguous stretches of sequence with no gaps. Additional information from long range data such as mate pair libraries, linked reads, Hi C, or optical maps allows contigs to be ordered and oriented into scaffolds that approximate chromosomes.

Quality assessment is critical. Metrics such as N50, total assembly length, and the number of contigs provide basic structure, while gene content analyses test biological completeness. Persistent challenges include segmental duplications, centromeres, telomeres, and other highly repetitive or structurally complex regions.

Recent advances aim at producing telomere to telomere assemblies, capturing diploid variation by phasing maternal and paternal haplotypes, and improving algorithms to handle large genomes efficiently. These developments are transforming fields from evolutionary biology and agriculture to medical genetics by delivering increasingly accurate reference genomes and enabling precise variant discovery.