A Genome Scaffold Algorithm for Extending Repetitive and Non-repetitive Contigs

The next generation sequencing platform produces massive short reads data. It is needed to assemble these short reads for further analysis. Unfortunately, gene assembly algorithm is still faced by a variety of complex challenges, especially for repetitive sequences. Based on De Bruijn Graph and SWA, we proposed a new genome scaffold algorithm named HashRepScaffold for extending repetitive contigs and non-repetitive contigs. By aligning original reads back to both ends of repetitive contigs and non-repetitive contigs, HashRepScaffold finds the best repetitive contig to exend the non-repetitive contig. Finally, simulation study was used to evaluate the performances of HashRepScaffold. The results indicated that HashRepScaffold have an excellent performances in extending repetitive and non-repetitive contigs.