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.
CITATION STYLE
Tischler-Höhle, G. (2019). Haplotype and repeat separation in long reads. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 10834 LNBI, pp. 103–114). Springer Verlag. https://doi.org/10.1007/978-3-030-14160-8_11
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