Genome Assembly

Abstract

Genome assembly uses sequence similarity to go from sequencing reads to longer contiguous sequences (contigs). Scaffolds are contigs linked together by gaps where the order and orientation of the contigs is known but the exact sequence connecting two contigs is unknown, represented by Ns which estimate the gap length. Here we describe recommendations for genome assembly for different sequencing technologies, describe organelle assembly, and review how to perform assembly quality control.

Keywords: Assembly; Contigs; Genomics; Overlap–layout–consensus; Ploidy; Scaffolds; Sequencing; String graph; de Bruijn graph; k-mer.