title: Hybrid assembly of the large and highly repetitive genome ofAegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm.
abstract: Long sequencing reads generated by single-molecule sequencing technology offer the possibility of dramatically improving the contiguity of genome assemblies. The biggest challenge today is that long reads have relatively high error rates, currently around 15%. The high error rates make it difficult to use this data alone, particularly with highly repetitive plant genomes. Errors in the raw data can lead to insertion or deletion errors (indels) in the consensus genome sequence, which in turn create significant problems for downstream analysis; for example, a single indel may shift the reading frame and incorrectly truncate a protein sequence. Here, we describe an algorithm that solves the high error rate problem by combining long, high-error reads with shorter but much more accurate Illumina sequencing reads, whose error rates average <1%. Our hybrid assembly algorithm combines these two types of reads to constructmega-reads, which are both long and accurate, and then assembles the mega-reads using the CABOG assembler, which was designed for long reads. We apply this technique to a large data set of Illumina and PacBio sequences from the speciesAegilops tauschii, a large and extremely repetitive plant genome that has resisted previous attempts at assembly. We show that the resulting assembled contigs are far larger than in any previous assembly, with an N50 contig size of 486,807 nucleotides. We compare the contigs to independently produced optical maps to evaluate their large-scale accuracy, and to a set of high-quality bacterial artificial chromosome (BAC)-based assemblies to evaluate base-level accuracy.
authors.affiliation: Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.|Institute for Physical Sciences and Technology, University of Maryland, College Park, Maryland 20742, USA.
authors.forename: Aleksey V
authors.initials: AV
authors.lastname: Zimin
authors.affiliation: Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.
authors.forename: Daniela
authors.initials: D
authors.lastname: Puiu
authors.affiliation: Department of Plant Sciences, University of California, Davis, California 95616, USA.
authors.forename: Ming-Cheng
authors.initials: MC
authors.lastname: Luo
authors.affiliation: Department of Plant Sciences, University of California, Davis, California 95616, USA.
authors.forename: Tingting
authors.initials: T
authors.lastname: Zhu
authors.affiliation: National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
authors.forename: Sergey
authors.initials: S
authors.lastname: Koren
authors.affiliation: Institute for Physical Sciences and Technology, University of Maryland, College Park, Maryland 20742, USA.|Department of Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Marçais
authors.affiliation: Institute for Physical Sciences and Technology, University of Maryland, College Park, Maryland 20742, USA.|Departments of Mathematics and Physics, University of Maryland, College Park, Maryland 20742, USA.
authors.forename: James A
authors.initials: JA
authors.lastname: Yorke
authors.affiliation: Department of Plant Sciences, University of California, Davis, California 95616, USA.
authors.forename: Jan
authors.initials: J
authors.lastname: Dvořák
authors.affiliation: Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.|Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University, Baltimore, Maryland 21218, USA.
authors.forename: Steven L
authors.initials: SL
authors.lastname: Salzberg
mesh_terms: D020451:Contig Mapping / Q000379:methods* / Q000592:standards; D059646:Genome Size; D018745:Genome, Plant; D023281:Genomics / Q000379:methods* / Q000592:standards; D006109:Poaceae / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA / Q000379:methods* / Q000592:standards; D012984:Software