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Evènement pour le groupe BioInformatique et Visualisation
Date | 2012-11-19 14:00-15:30 |
Titre | Efficient data structures for large-scale genome sequencing data. |
Résumé | To assemble and/or detect variants in large-scale genomics data, an algorithmic
ingredient of choice is the de Bruijn graph. On large datasets, analyzing
such graph requires a significant amount of system memory.
This talk deals with ultra-low memory representation of de Bruijn graphs.
We propose a new encoding, which occupies an order of magnitude less space
than current representations. The encoding is based on a Bloom filter, with
an additional structure to remove critical false positives. An assembly
software implementing this structure, Minia, performed a complete de novo
assembly of human genome short reads using 5.7 Gb of memory in 23 hours.
The article (and in the near future, the public source code) can be found
on the webpage of Minia: http://minia.genouest.org/ |
Lieu | salle de réunion Sud, CGFB |
Orateur | Guillaume Rizk |
Email | macha@labri.fr |
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