Algorithms for Next-Generation Sequencing Data Techniques, Approache
The 14 contributed chapters in this book survey the most recent developments in high-performance algorithms for NGS data, offering fundamental insights and technical information specifically on indexing, compression and storage; error correction; alignmen
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Algorithms for Next-Generation Sequencing Data Techniques, Approaches, and Applications
Algorithms for Next-Generation Sequencing Data
Mourad Elloumi Editor
Algorithms for Next-Generation Sequencing Data Techniques, Approaches, and Applications
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Editor Mourad Elloumi LaTICE Tunis, Tunisia University of Tunis-El Manar Tunis, Tunisia
ISBN 978-3-319-59824-6 DOI 10.1007/978-3-319-59826-0
ISBN 978-3-319-59826-0 (eBook)
Library of Congress Control Number: 2017950216 © Springer International Publishing AG 2017 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Printed on acid-free paper This Springer imprint is published by Springer Nature The registered company is Springer International Publishing AG The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland
To my parents and my children.
Preface
A deoxyribonucleic acid (DNA) macromolecule can be coded by a sequence over a four-letter alphabet. These letters are A, C, G, and T, and they code respectively the bases Adenine, Cytosine, Guanine and Thymine. DNA sequencing consists then in determining the exact order of these bases in a DNA macromolecule. As a matter of fact, DNA sequencing technology is playing a key role in the advancement of molecular biology. Compared to previous sequencing machines, Next-Generation Sequencing (NGS) machines function much faster, with significantly lower production costs and much higher throughput in the form of short reads, i.e., short sequences coding portions of DNA macromolecules. As a result of the extended spread of NGS machines, we are witnessing an exponential growth in the number of newly available short reads. Hence, we are facing the challenge of storing them to analyze huge numbers of reads representing sets of portions of genomes, or even whole genomes. The analysis of this huge number of reads will help, among others, to decode life’s my
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