4.3.4.2 Divide and conquer with the enhanced pigeonhole principle. Įstimating the lower bound of the number of mismatches. 4.3 Align reads allowing a small number of mismatches 4.3.1 Mismatch seed hashing approach. 4.2.2 Mapping reads with a quality score. 4.2.1 Mapping reads with no quality score. 4.2 Overview of the read mapping problem. 3.5.4 Simulate a suffix trie using the FM-index.
3.5.3.1 Inverting the BWT B to the original text T 3.5.3.2 Simulate a suffix array using the FM-index 3.5.3.3 Pattern matching. 3.4.4 Estimating the similarity of two sets using minHash 3.5 Full-text index. 3.4.3 Maintain a multiset using a counting Bloom filter. 3.4.2 Maintain a set using a Bloom filter. 3.4.1 Maintain an associative array by simple hashing. 3.3.2 Unobserved variable and EM algorithm. ģ Related algorithms and data structures 3.1 Introduction. 2.6 Format for representing density data 2.7 Exercises. 1.6 Comparison of the three generations of sequencing. 1.5.3 Direct imaging of DNA using electron microscopy. 1.5.1 Single-molecule real-time sequencing.
1.4.4 Polymerase-mediated methods based on unmodified nucleotides. 1.4.3 Polymerase-mediated methods based on reversible terminator nucleotides. Algorithms for Next-Generation Sequencing Wing-Kin SungĬRC Press Taylor & Francis Group 6000 Broken Sound Parkway NW, Suite 300 Boca Raton, FL 33487-2742 © 2017 by Taylor & Francis Group, LLC CRC Press is an imprint of Taylor & Francis Group, an Informa business Printed on acid-free paper Version Date: 20170421 International Standard Book Number-13: 978-1-4665-6550-0 (Hardback) Visit the Taylor & Francis Web site at and the CRC Press Web site at ġ Introduction 1.1 DNA, RNA, protein and cells.
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