RT Journal Article
SR Electronic
T1 Haplotype and Repeat Separation in Long Reads
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 145474
DO 10.1101/145474
A1 German Tischler
YR 2017
UL http://biorxiv.org/content/early/2017/06/02/145474.abstract
AB 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 amount of difference between the similar regions we want to separate. Our methods can separate read classes stemming from regions with as little as 1% difference.