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The eukaryotic genome, its reads, and the unfinished assembly

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Muñoz, José Fernando
Gallo, Juan Esteban
Misas, Elizabeth
McEwen, Juan Guillermo
Clay, Oliver Keatinge

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2013

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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. © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.
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Accuracy , Algorithm , Article , Bioinformatics , Fungal genome , Fungal strain , Genome analysis , Human , Information processing , Information retrieval , Next generation sequencing , Nonhuman , Priority journal , Reliability , Reproducibility , Sequence analysis , Animals , Base sequence , Chromosome mapping , Eukaryota , Genome , Genomics , High-throughput nucleotide sequencing , Humans , Molecular sequence annotation , Sequence analysis , Eukaryota , Assembly-free genome analysis , Eukaryotic genomics , Microbial strain collection , Next generation sequencing , Object-view separation
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