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2019 | OriginalPaper | Chapter

Haplotype and Repeat Separation in Long Reads

Author : German Tischler-Höhle

Published in: Computational Intelligence Methods for Bioinformatics and Biostatistics

Publisher: Springer International Publishing

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Abstract

Resolving the correct structure and succession of highly similar sequence stretches is one of the main open problems in genome assembly. For non haploid genomes this includes determining the sequences of the different haplotypes. For all but the smallest genomes it also involves separating different repeat instances. In this paper we discuss methods for resolving such problems in third generation long reads by classifying alignments between long reads according to whether they represent true or false read overlaps. The main problem in this context is the high error rate found in such reads, which greatly exceeds the variance between the similar regions we want to separate. Our methods can separate read classes stemming from regions with as little as \(1\%\) difference.

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Title: Haplotype and Repeat Separation in Long Reads
Author: German Tischler-Höhle
Publisher: Springer International Publishing
Book: Computational Intelligence Methods for Bioinformatics and Biostatistics
Print ISBN: 978-3-030-14159-2

Electronic ISBN: 978-3-030-14160-8

Copyright Year: 2019
DOI: https://doi.org/10.1007/978-3-030-14160-8_11

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