Assembly of large genomes using second-generation sequencing

Abstract

Second-generation sequencing technology can now be used to sequence an entire human genome in a matter of days and at low cost. Sequence read lengths, initially very short, have rapidly increased since the technology first appeared, and we now are seeing a growing number of efforts to sequence large genomes de novo from these short reads. In this Perspective, we describe the issues associated with short-read assembly, the different types of data produced by second-gen sequencers, and the latest assembly algorithms designed for these data. We also review the genomes that have been assembled recently from short reads and make recommendations for sequencing strategies that will yield a high-quality assembly.

Figure 1.

The k-mer uniqueness ratio for five well-known organisms and one single-celled human parasite. The ratio is defined here as the percentage of the genome that is covered by unique sequences of length k or longer. The horizontal axis shows the length in base pairs of the sequences. For example, ∼92.5% of the grapevine genome is contained in unique sequences of 100 bp or longer.

Figure 2.

Differences between an overlap graph and a de Bruijn graph for assembly. Based on the set of 10 8-bp reads (A), we can build an overlap graph (B) in which each read is a node, and overlaps >5 bp are indicated by directed edges. Transitive overlaps, which are implied by other longer overlaps, are shown as dotted edges. In a de Bruin graph (C), a node is created for every k-mer in all the reads; here the k-mer size is 3. Edges are drawn between every pair of successive k-mers in a read, where the k-mers overlap by k − 1 bases. In both approaches, repeat sequences create a fork in the graph. Note here we have only considered the forward orientation of each sequence to simplify the figure.

Figure 3.

Expected average contig length for a range of different read lengths and coverage values. Also shown are the average contig lengths and N50 lengths for the dog genome, assembled with 710-bp reads, and the panda genome, assembled with reads averaging 52 bp in length.