14:ff:whatsapp:cibb (In proceedings)
|
Author(s) | Marco Aldinucci, Andrea Bracciali, Tobias Marschall, Murray Patterson, Nadia Pisanti and Massimo Torquati |
Title | « High-Performance Haplotype Assembly » |
In | Proc. of the 11th Intl. meeting on Computational Intelligence methods for Bioinformatics and Biostatistics (CIBB) |
Series | LNBI |
Year | 2014 |
Publisher | Springer |
Address | Cambridge, UK |
Abstract & Keywords |
The problem of Haplotype Assembly is an essential step in human genome analysis. Being the well known MEC model for its solution NP-hard, it is currently addressed by using algorithms that grow exponentially with the length of DNA fragments obtained by the sequencing process. Technological improvements will reduce fragmenta- tion, increase fragment length and make such computational costs worst. WhatsHap is a recently proposed novel approach which moves complex- ity from fragment length to fragment sovrapposition, improving the per- spective of computational costs, but Haplotype Assembly still remains a demanding computational problem. A methodological approach towards high-performance computing WhatsHap is discussed in this paper.
Keywords: fastflow
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@inproceedings{14:ff:whatsapp:cibb,
month = jun,
author = {Marco Aldinucci and Andrea Bracciali and Tobias Marschall and Murray
Patterson and Nadia Pisanti and Massimo Torquati},
series = {{LNBI}},
keywords = {fastflow},
booktitle = {Proc. of the 11th Intl. meeting on Computational Intelligence
methods for Bioinformatics and Biostatistics (CIBB)},
abstract = {The problem of Haplotype Assembly is an essential step in human
genome analysis. Being the well known MEC model for its solution
NP-hard, it is currently addressed by using algorithms that grow
exponentially with the length of DNA fragments obtained by the
sequencing process. Technological improvements will reduce
fragmenta- tion, increase fragment length and make such
computational costs worst. WhatsHap is a recently proposed novel
approach which moves complex- ity from fragment length to fragment
sovrapposition, improving the per- spective of computational
costs, but Haplotype Assembly still remains a demanding
computational problem. A methodological approach towards
high-performance computing WhatsHap is discussed in this paper. },
address = {Cambridge, UK},
title = {High-Performance Haplotype Assembly},
publisher = {Springer},
year = {2014},
}
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