Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

Although many de novo genome assembly projects have recently been conducted using high-throughput sequencers, assembling highly heterozygous diploid genomes is a substantial challenge due to the increased complexity of the de Bruijn graph structure predominantly used. To address the increasing demand for sequencing of nonmodel and/or wild-type samples, in most cases inbred lines or fosmid-based hierarchical sequencing methods are used to overcome such problems. However, these methods are costly and time consuming, forfeiting the advantages of massive parallel sequencing. Here, we describe a novel de novo assembler, Platanus, that can effectively manage high-throughput data from heterozygous samples. Platanus…

• MO
  Ministry of Education, Culture, Sports, Science and Technology

  Awards: 22125008, No. 221S0002, 221S0002, 24310142
• JS
  Japan Society for the Promotion of Science

  Awards: No. 221S0002, 24310142, 221S0002