Correction of long sequencing reads: a novel approach: Abstract for the keynote presentation at " From Nucleotides to Networks " Symposium, Ghent, Belgium.

Eric Rivals 1, 2
2 MAB - Méthodes et Algorithmes pour la Bioinformatique
LIRMM - Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier
Abstract : High-throughput DNA and RNA sequencing has become a routine experiment in molecular biology and life sciences in general. It is increasingly used in the hospital as a key procedure of personalized medicine. Compared to the second generation, third generation sequencing technologies produce longer reads with comparatively lower throughput and higher error rate. Those errors include substitutions, in-dels, and they hinder or at least complicate downstream analysis like mapping or de novo assembly. However, these long read data are often used in conjunction with short reads of the 2nd generation. I will present a hybrid strategy for correcting the long reads using the short reads that we introduced last year. Unlike existing error correction tool, ours, called LoRDEC, avoids the alignment of short reads on long reads, which is computationally very intensive. Instead, it takes advantage of a succinct graph to represent the short reads, and compares the long reads to paths in the graph. Experiments show that LoRDEC outperforms existing methods in running time and memory while achieving a comparable correction performance. In conclusion, i will comment on the impact of read error correction. LoRDEC is available at http://atgc.lirmm.fr/lordec and is a joint work with Leena Salmela.
Type de document :
Communication dans un congrès
Symposium "From Nucleotides to Networks", May 2015, Gand (Ghent), Belgium. 2015, 〈http://www.bign2n.ugent.be〉
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https://hal-lirmm.ccsd.cnrs.fr/lirmm-01185688
Contributeur : Eric Rivals <>
Soumis le : vendredi 21 août 2015 - 10:44:01
Dernière modification le : jeudi 11 janvier 2018 - 06:26:13

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  • HAL Id : lirmm-01185688, version 1

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Eric Rivals. Correction of long sequencing reads: a novel approach: Abstract for the keynote presentation at " From Nucleotides to Networks " Symposium, Ghent, Belgium.. Symposium "From Nucleotides to Networks", May 2015, Gand (Ghent), Belgium. 2015, 〈http://www.bign2n.ugent.be〉. 〈lirmm-01185688〉

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