A De Novo Genome Assembly Algorithm for Repeats and Nonrepeats

Figure 1

High-level diagram of the SWA assembly pipeline. The assembly has three main modules: preparatory stage, constructing repeats, and constructing nonrepeats. Preparatory stage includes data cleaning, unique processing, and hash index constructing. The stage of constructing repeats and constructing nonrepeats can be performed in parallel or in series. Figure 1 shows the parallel manner. The specific steps of constructing repeats and nonrepeats are detailed in Methods.