@inproceedings{3069e099d83e42b5a69f5d690cafb90d,
title = "High performance computing for haplotyping: models and platforms",
abstract = "The reconstruction of the haplotype pair for each chromosome is a hot topic in Bioinformatics and Genome Analysis. In Haplotype Assembly (HA), all heterozygous Single Nucleotide Polymorphisms (SNPs) have to be assigned to exactly one of the two chromosomes. In this work, we outline the state-of-the-art on HA approaches and present an in-depth analysis of the computational performance of GenHap, a recent method based on Genetic Algorithms. GenHap was designed to tackle the computational complexity of the HA problem by means of a divide-et-impera strategy that effectively leverages multi-core architectures. In order to evaluate GenHap{\textquoteright}s performance, we generated different instances of synthetic (yet realistic) data exploiting empirical error models of four different sequencing platforms (namely, Illumina NovaSeq, Roche/454, PacBio RS II and Oxford Nanopore Technologies MinION). Our results show that the processing time generally decreases along with the read length, involving a lower number of sub-problems to be distributed on multiple cores.",
keywords = "Future-generation sequencing, Genome Analysis Haplotype Assembly, High Performance Computing, Master-Slave paradigm",
author = "Andrea Tangherloni and Leonardo Rundo and Simone Spolaor and Nobile, \{Marco S.\} and Ivan Merelli and Daniela Besozzi and Giancarlo Mauri and Paolo Cazzaniga and Pietro Li{\`o}",
year = "2019",
month = jan,
day = "1",
doi = "10.1007/978-3-030-10549-5\_51",
language = "English",
isbn = "978-3-030-10548-8",
series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",
publisher = "Springer",
pages = "650--661",
editor = "Gabriele Mencagli and Heras, \{Dora B.\}",
booktitle = "Euro-Par 2018",
address = "Germany",
note = "24th International Conference on Parallel and Distributed Computing, Euro-Par 2018 ; Conference date: 27-08-2018 Through 28-08-2018",
}