Research output

Conference Paper (in Formal Publication) ()

High-Performance Haplotype Assembly

Citation
Aldinucci M, Bracciali A, Marschall T, Patterson M, Pisanti N & Torquati M (2015) High-Performance Haplotype Assembly In: Serio CDI, Lio P, Nonis A, Tagliaferri R (ed.) Computational Intelligence Methods for Bioinformatics and Biostatistics: 11th International Meeting, CIBB 2014, Cambridge, UK, June 26-28, 2014, Revised Selected Papers, Cham, Switzerland: Springer. 11th International Meeting, CIBB 2014, 26.6.2014 - 28.6.2014, Cambridge, pp. 245-258.

Abstract
The problem ofHaplotype Assemblyis an essential step in human genome analysis. It is typically formalised as theMinimum Error Correction(MEC) problem which is NP-hard. MEC has been approached using heuristics, integer linear programming, and fixed-parameter tractability (FPT), including approaches whose runtime is exponential in the length of the DNA fragments obtained by the sequencing process. Technological improvements are currently increasing fragment length, which drastically elevates computational costs for such methods. We presentpWhatsHap, a multi-core parallelisation ofWhatsHap, a recent FPT optimal approach to MEC.WhatsHapmoves complexity from fragment length to fragment overlap and is hence of particular interest when considering sequencing technology’s current trends.pWhatsHapfurther improves the efficiency in solving the MEC problem, as shown by experiments performed on datasets with high coverage.

StatusPublished
EditorSerio CDI, Lio P, Nonis A, Tagliaferri R
AuthorsAldinucci Marco, Bracciali Andrea, Marschall Tobias, Patterson Murray, Pisanti Nadia, Torquati Massimo
Title of seriesLecture Notes in Computer Science
Number in series8623
Publication date2015
Date of public distribution06/2014
URLhttp://link.springer.com/…3-319-24462-4_21
PublisherSpringer
Place of publicationCham, Switzerland
ISSN of series 0302-9743
ISBN 978-3-319-24461-7
eISBN 978-3-319-24462-4
LanguageEnglish
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