Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study

Cerdeira LT, Carneiro AR, Juca Ramos RT, de Almeida SS, D'Afonseca V, Cruz Schneider MP, Baumbach J, Tauch A, McCulloch JA, Carvalho Azevedo VA, Silva A (2011)
Journal of Microbiological Methods 86(2): 218-223.

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Abstract
Due to the advent of the so-called Next-Generation Sequencing (NGS) technologies the amount of monetary and temporal resources for whole-genome sequencing has been reduced by several orders of magnitude. Sequence reads can be assembled either by anchoring them directly onto an available reference genome (classical reference assembly), or can be concatenated by overlap (de novo assembly). The latter strategy is preferable because it tends to maintain the architecture of the genome sequence the however, depending on the NGS platform used, the shortness of read lengths cause tremendous problems the in the subsequent genome assembly phase, impeding closing of the entire genome sequence. To address the problem, we developed a multi-pronged hybrid de nova strategy combining De Bruijn graph and Overlap-Layout-Consensus methods, which was used to assemble from short reads the entire genome of Corynebacterium pseudotuberculosis strain 119, a bacterium with immense importance in veterinary medicine that causes Caseous Lymphadenitis in ruminants, principally ovines and caprines. Briefly, contigs were assembled de novo from the short reads and were only oriented using a reference genome by anchoring. Remaining gaps were closed using iterative anchoring of short reads by craning to gap flanks. Finally, we compare the genome sequence assembled using our hybrid strategy to a classical reference assembly using the same data as input and show that with the availability of a reference genome, it pays off to use the hybrid de nova strategy, rather than a classical reference assembly, because more genome sequences are preserved using the former. (C) 2011 Elsevier B.V. All rights reserved.
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Cerdeira LT, Carneiro AR, Juca Ramos RT, et al. Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study. Journal of Microbiological Methods. 2011;86(2):218-223.
Cerdeira, L. T., Carneiro, A. R., Juca Ramos, R. T., de Almeida, S. S., D'Afonseca, V., Cruz Schneider, M. P., Baumbach, J., et al. (2011). Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study. Journal of Microbiological Methods, 86(2), 218-223. doi:10.1016/j.mimet.2011.05.008
Cerdeira, L. T., Carneiro, A. R., Juca Ramos, R. T., de Almeida, S. S., D'Afonseca, V., Cruz Schneider, M. P., Baumbach, J., Tauch, A., McCulloch, J. A., Carvalho Azevedo, V. A., et al. (2011). Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study. Journal of Microbiological Methods 86, 218-223.
Cerdeira, L.T., et al., 2011. Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study. Journal of Microbiological Methods, 86(2), p 218-223.
L.T. Cerdeira, et al., “Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study”, Journal of Microbiological Methods, vol. 86, 2011, pp. 218-223.
Cerdeira, L.T., Carneiro, A.R., Juca Ramos, R.T., de Almeida, S.S., D'Afonseca, V., Cruz Schneider, M.P., Baumbach, J., Tauch, A., McCulloch, J.A., Carvalho Azevedo, V.A., Silva, A.: Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study. Journal of Microbiological Methods. 86, 218-223 (2011).
Cerdeira, Louise Teixeira, Carneiro, Adriana Ribeiro, Juca Ramos, Rommel Thiago, de Almeida, Sintia Silva, D'Afonseca, Vivian, Cruz Schneider, Maria Paula, Baumbach, Jan, Tauch, Andreas, McCulloch, John Anthony, Carvalho Azevedo, Vasco Ariston, and Silva, Artur. “Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study”. Journal of Microbiological Methods 86.2 (2011): 218-223.
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Whole genome sequencing of environmental Vibrio cholerae O1 from 10 nanograms of DNA using short reads.
Pérez Chaparro PJ, McCulloch JA, Cerdeira LT, Al-Dilaimi A, Canto de Sá LL, de Oliveira R, Tauch A, de Carvalho Azevedo VA, Cruz Schneider MP, da Silva AL., J Microbiol Methods 87(2), 2011
PMID: 21871929

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