TY - GEN
T1 - Limits to sequencing and de novo assembly
T2 - 2nd Colombian Congress on Computational Biology and Bioinformatics, CCBCOL 2013
AU - Muñnoz, Jośe Fernando
AU - Misas, Elizabeth
AU - Gallo, Juan Esteban
AU - McEwen, Juan Guillermo
AU - Clay, Oliver Keatinge
PY - 2014/1/1
Y1 - 2014/1/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84894870251&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84894870251&partnerID=8YFLogxK
U2 - 10.1007/978-3-319-01568-2_32
DO - 10.1007/978-3-319-01568-2_32
M3 - Conference contribution
AN - SCOPUS:84894870251
SN - 9783319015675
T3 - Advances in Intelligent Systems and Computing
SP - 221
EP - 230
BT - Advances in Computational Biology - Proceedings of the 2nd Colombian Congress on Computational Biology and Bioinformatics CCBCOL 2013
PB - Springer
Y2 - 25 September 2013 through 27 September 2013
ER -