title: The eukaryotic genome, its reads, and the unfinished assembly.
abstract: In recent years, readily affordable short read sequences provided by next-generation sequencing (NGS) have become longer and more accurate. This has led to a jump in interest in the utility of NGS-only approaches for exploring eukaryotic genomes. The concept of a static, 'finished' genome assembly, which still appears to be a faraway goal for many eukaryotes, is yielding to new paradigms. We here motivate an object-view concept where the raw reads are the main, fixed object, and assemblies with their annotations take a role of dynamically changing and modifiable views of that object.
authors.affiliation: Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia.
authors.forename: José Fernando
authors.initials: JF
authors.lastname: Muñoz
authors.forename: Juan Esteban
authors.initials: JE
authors.lastname: Gallo
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Misas
authors.forename: Juan Guillermo
authors.initials: JG
authors.lastname: McEwen
authors.forename: Oliver Keatinge
authors.initials: OK
authors.lastname: Clay
mesh_terms: D000818:Animals; D001483:Base Sequence; D002874:Chromosome Mapping; D056890:Eukaryota; D015894:Genome, Human; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D058977:Molecular Sequence Annotation; D017422:Sequence Analysis, DNA