Limits to sequencing and de novo assembly: Classic benchmark sequences for optimizing fungal NGS designs

Jośe Fernando Muñnoz, Elizabeth Misas, Juan Esteban Gallo, Juan Guillermo McEwen, Oliver Keatinge Clay

Resultado de la investigación: Capítulo en Libro/Reporte/ConferenciaContribución a la conferencia

3 Citas (Scopus)

Resumen

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.

Idioma originalInglés estadounidense
Título de la publicación alojadaAdvances in Computational Biology - Proceedings of the 2nd Colombian Congress on Computational Biology and Bioinformatics CCBCOL 2013
EditorialSpringer
Páginas221-230
Número de páginas10
ISBN (versión impresa)9783319015675
DOI
EstadoPublicada - ene. 1 2014
Evento2nd Colombian Congress on Computational Biology and Bioinformatics, CCBCOL 2013 - Manizales, Colombia
Duración: sept. 25 2013sept. 27 2013

Serie de la publicación

NombreAdvances in Intelligent Systems and Computing
Volumen232
ISSN (versión impresa)2194-5357

Conferencia

Conferencia2nd Colombian Congress on Computational Biology and Bioinformatics, CCBCOL 2013
País/TerritorioColombia
CiudadManizales
Período9/25/139/27/13

Áreas temáticas de ASJC Scopus

  • Ingeniería de control y sistemas
  • Informática (todo)

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