Fig 1. Overview of the genome assembly process.

First, genetic material is sequenced, generating a collection of sequenced fragments (reads). These reads are processed by a computer program called an assembler, which merges the reads based on their overlap to construct larger contigs. Contigs are then oriented and ordered with respect to each other with a computer program called a scaffolder, relying on a variety of sources of linkage information. The scaffolds provide information about the long-range structure of the genome without specifying the actual DNA sequence within the gaps between contigs. The size of the gaps can also only be approximately estimated. contig, contiguous genomic segment.