De novo

De novo assembly refers to the process of aligning many DNA sequencing reads to one another in order to determine overlap between reads. These are used to construct longer and longer assemblies of DNA sequences. Unfortunately, due to the fact that nearly every genome contains repeated sequences, and these repeats are often longer than the average length of the DNA sequencing reads, generating fully assembled genomes is not currently feasible for most genomes. Individual sequences that are partially assembled genomes are often called contigs, scaffolds, and superscaffolds.