title: Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage.
abstract: Genome assemblies that are accurate, complete and contiguous are essential for identifying important structural and functional elements of genomes and for identifying genetic variation. Nevertheless, most recent genome assemblies remain incomplete and fragmented. While long molecule sequencing promises to deliver more complete genome assemblies with fewer gaps, concerns about error rates, low yields, stringent DNA requirements and uncertainty about best practices may discourage many investigators from adopting this technology. Here, in conjunction with the platinum standard Drosophila melanogaster reference genome, we analyze recently published long molecule sequencing data to identify what governs completeness and contiguity of genome assemblies. We also present a hybrid meta-assembly approach that achieves remarkable assembly contiguity for both Drosophila and human assemblies with only modest long molecule sequencing coverage. Our results motivate a set of preliminary best practices for obtaining accurate and contiguous assemblies, a 'missing manual' that guides key decisions in building high quality de novo genome assemblies, from DNA isolation to polishing the assembly.
authors.affiliation: Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA 92697, USA.
authors.forename: Mahul
authors.initials: M
authors.lastname: Chakraborty
authors.affiliation: Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA 92697, USA.
authors.forename: James G
authors.initials: JG
authors.lastname: Baldwin-Brown
authors.affiliation: Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA 92697, USA.|Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA.
authors.forename: Anthony D
authors.initials: AD
authors.lastname: Long
authors.affiliation: Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA 92697, USA jje@uci.edu.|Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA.
authors.forename: J J
authors.initials: JJ
authors.lastname: Emerson
mesh_terms: D000818:Animals; D002460:Cell Line; D019295:Computational Biology / Q000379:methods; D004331:Drosophila melanogaster / Q000235:genetics; D016678:Genome; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D017422:Sequence Analysis, DNA