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A multi-objective optimisation approach to the design of experiment in de novo assembly projects
KTH, Skolan för datavetenskap och kommunikation (CSC). KTH, Centra, Science for Life Laboratory, SciLifeLab.
2012 (engelsk)Inngår i: Database and Expert Systems Applications (DEXA), 2012 23rd International Workshop on, IEEE , 2012, s. 213-217Konferansepaper, Publicerat paper (Fagfellevurdert)
Abstract [en]

Genomics projects are characterised by difficult biological pipelines and high sequencing costs. In particular, de novo assembly projects must go through data production, assembly, and results validation. Early mistakes in the first (and most expensive) step can therefore be detected only at a very late stage and have serious consequences. Our goal is to design a pipeline able to provide the users with the optimal input for the sequencing experiments within a de novo assembly project. We present a new approach, based on multi-objective optimisation, aiming at transforming the design of genomics experiments from a set of "best practices" to an algorithmically controlled procedure. We implemented our model with mode FRONTIER and we show how our method can be used to infer the final quality of a whole genome assembly project from the results obtained on a small but representative sample.

sted, utgiver, år, opplag, sider
IEEE , 2012. s. 213-217
Serie
Proceedings - International Workshop on Database and Expert Systems Applications, DEXA, ISSN 1529-4188
Emneord [en]
de novo assembly, multi-objective optimisation, Pareto optima, sequencing technologies
HSV kategori
Identifikatorer
URN: urn:nbn:se:kth:diva-108030DOI: 10.1109/DEXA.2012.42ISI: 000312658400034Scopus ID: 2-s2.0-84869435177ISBN: 978-076954801-2 (tryckt)OAI: oai:DiVA.org:kth-108030DiVA, id: diva2:580172
Konferanse
23rd International Workshop on Database and Expert Systems Applications, DEXA 2012, 3 September 2012 through 6 September 2012, Vienna
Forskningsfinansiär
Science for Life Laboratory - a national resource center for high-throughput molecular bioscienceSwedish e‐Science Research Center
Merknad

QC 20121221

Tilgjengelig fra: 2012-12-21 Laget: 2012-12-19 Sist oppdatert: 2018-01-11bibliografisk kontrollert

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