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

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Scopus citations

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.

Original languageEnglish (US)
Title of host publicationAdvances in Computational Biology - Proceedings of the 2nd Colombian Congress on Computational Biology and Bioinformatics CCBCOL 2013
PublisherSpringer
Pages221-230
Number of pages10
ISBN (Print)9783319015675
DOIs
StatePublished - Jan 1 2014
Event2nd Colombian Congress on Computational Biology and Bioinformatics, CCBCOL 2013 - Manizales, Colombia
Duration: Sep 25 2013Sep 27 2013

Publication series

NameAdvances in Intelligent Systems and Computing
Volume232
ISSN (Print)2194-5357

Conference

Conference2nd Colombian Congress on Computational Biology and Bioinformatics, CCBCOL 2013
Country/TerritoryColombia
CityManizales
Period9/25/139/27/13

All Science Journal Classification (ASJC) codes

  • Control and Systems Engineering
  • Computer Science(all)

Fingerprint

Dive into the research topics of 'Limits to sequencing and de novo assembly: Classic benchmark sequences for optimizing fungal NGS designs'. Together they form a unique fingerprint.

Cite this