@inproceedings{6770b7f9b995422c8359b398c0ec77ee,
title = "Translocator: Local realignment and global remapping enabling accurate translocation detection using single-molecule sequencing long reads",
abstract = "Translocation is an important class of structural variants known to be associated with cancer formation and treatment. The recent development in single-molecule sequencing technologies that produce long reads has promised an advance in detecting translocations accurately. However, existing tools struggled with the high base error-rate of the long reads. Figuring out the correct translocation breakpoints is especially challenging due to suboptimally aligned reads. To address the problem, we developed Translocator, a robust and accurate translocation detection method that implements an effective realignment algorithm to recover the correct alignments. For benchmarking, we analyzed using NA12878 long reads against a modified GRCh38 reference genome embedded with translocations at known locations. Our results show that Translocator significantly outperformed other state-of-The-Art methods, including Sniffles and PBSV. On Oxford Nanopore data, the recall improved from 48.2% to 87.5% and the precision from 88.7% to 92.7%. Translocator is available open-source at https://github.com/HKU-BAL/Translocator.",
keywords = "Global Remapping, Local realignment, Structural Variant, Translocation",
author = "Ye Wu and Ruibang Luo and Lam, {Tak Wah} and Ting, {Hing Fung} and Junwen Wang",
note = "Publisher Copyright: {\textcopyright} 2020 ACM.; 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, BCB 2020 ; Conference date: 21-09-2020 Through 24-09-2020",
year = "2020",
month = sep,
day = "21",
doi = "10.1145/3388440.3412457",
language = "English (US)",
series = "Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, BCB 2020",
publisher = "Association for Computing Machinery, Inc",
booktitle = "Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, BCB 2020",
}