@inproceedings{c44bdcee7a68480ba079690ca581aa29,
title = "Comparative analysis of alignment tools for nanopore reads",
abstract = "Alignment of sequence reads is an important step of many bioinformatics workflows. While the alignment of short reads is well investigated, the alignment of long reads produced by third-generation sequencing technologies, such as Oxford Nanopore, is more challenging because they have high error rates (10-40{\%}). Furthermore, due to their different algorithmic approaches, different tools produce varied alignments, significantly influencing the downstream analyses. In this study, we evaluated the performance of three alignment tools (LAST, GraphMap, and NanoBLASTer) using simulated nanopore reads. Although the three alignment strategies gave similar results (e.g., all close to 100{\%} precision), GraphMap reported the longest alignments while LAST the shortest. However, GraphMap showed the lowest recall (90{\%}) indicating high false negative rates. While GraphMap had the highest percentage of reads that were mapped to the correct reference regions, NanoBLASTer and especially LAST mapped the majority of the reads only partially correctly. Based on our multiple statistics, GraphMap had the best overall performance.",
keywords = "Oxford Nanopore, Third-generation sequencing, error rates, long-read alignment, precision, recall, resources",
author = "Natasha Pavlovikj and Moriyama, {Etsuko N.} and Deogun, {Jitender S.}",
year = "2017",
month = "12",
day = "15",
doi = "10.1109/BIBM.2017.8217645",
language = "English (US)",
series = "Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017",
publisher = "Institute of Electrical and Electronics Engineers Inc.",
pages = "169--174",
editor = "Illhoi Yoo and Zheng, {Jane Huiru} and Yang Gong and Hu, {Xiaohua Tony} and Chi-Ren Shyu and Yana Bromberg and Jean Gao and Dmitry Korkin",
booktitle = "Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017",
note = "2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017 ; Conference date: 13-11-2017 Through 16-11-2017",
}