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Aix-Marseille Université
Institut de Mathématiques de Marseille (I2M) - UMR 7373
Site Saint-Charles : 3 place Victor Hugo, Case 19, 13331 Marseille Cedex 3
Site Luminy : Campus de Luminy - Case 907 - 13288 Marseille Cedex 9

Séminaire

Correction of long sequencing reads: a novel approach




Date(s) : 27/01/2016   iCal
11h00 - 12h00

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, indels, 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.

http://www.lirmm.fr/~rivals/

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