On the other hand, the rearrangement-based scaffolding algorithms utilize the concept of genome rearrangements to scaffold the contigs of the target draft genome such that the sequence markers (or genes) shared between the scaffolded target and reference genomes have similar order and orientation as much as possible. The alignment-based scaffolding algorithms first align contigs in a target draft genome against a reference sequence and then scaffold the contigs according to the positions of their matches in the reference. The algorithms used to develop all these scaffolders can be classified into two main categories: the alignment-based algorithms and the rearrangement-based algorithms. So far, many such reference-based scaffolders have been proposed. The scaffolding process utilizes a genomic sequence available from a related organism to serve as a reference to scaffold the contigs of a draft genome. To further obtain more complete sequences of draft genomes, therefore, the contigs of the draft genomes usually are required to be ordered and oriented into scaffolds, which actually are larger gap-containing sequences whose gaps between the scaffolded contigs can be closed later in the gap-filling process. The availability of complete genomes actually is significant to the downstream analysis and interpretation of their sequences in many biological applications. Largely because of repetitive sequences, whose lengths are often larger than those of the reads, most of assembled sequences are just draft genomes that usually consists of several hundreds or even thousands of contigs (contiguous sequences). However, assembling a large number of reads generated from current NGS sequencing platforms into a complete genome still is a challenging job. Due to recent advances in next-generation sequencing (NGS) technologies, more and more genomes of organisms can be sequenced quickly at a moderate cost.

Genome scaffold tools