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Limits to sequencing and de novo assembly: Classic benchmark sequences for optimizing fungal NGS designs
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Autores
Muñoz, José Fernando
Misas, Elizabeth
Gallo, Juan Esteban
McEwen, Juan Guillermo
Clay, Oliver Keatinge
Fecha
2014
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Springer Verlag
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Abstract
Planning of pipelines for next-generation sequencing (NGS) projects could be facilitated by using simple DNA sequence benchmarks, i.e., standard test sequences that could monitor or help to predict ease or difficulty of (a) short-read sequencing and (b) de novo assembly of the sequenced reads. We propose that familiar, gene-sized sequences, including but not limited to nuclear protein-coding genes, would provide feasible consensus benchmarks allowing simple visualization. We illustrate our proposal for fungi with candidates from ribosomal DNA (rDNA, used in phylogeny and identification/diagnostics), mitochondrial DNA (mtDNA), and combinatorially constructed conceptual (synthetic) DNA sequences. The exploratory analysis of such familiar candidate loci could be a step toward finding, testing and establishing familiar, biologically interpretable consensus benchmark sequences for fungal and other eukaryotic genomes. © Springer International Publishing Switzerland 2014.
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Keywords
Benchmarking , Biology , DNA sequences , Genes , Nucleic acids , De novo assemblies , Eukaryotic genome , Exploratory analysis , Mitochondrial DNA (mtdna) , Next-generation sequencing , Protein-coding genes , Ribosomal DNA , Standard tests , Bioinformatics , Benchmarking , De novo assembly , Eukaryotic genomes , Next generation sequencing
