Comparative analysis of alignment tools for nanopore reads

Natasha Pavlovikj; Etsuko N. Moriyama; Jitender S. Deogun

doi:10.1109/BIBM.2017.8217645

Comparative analysis of alignment tools for nanopore reads

Natasha Pavlovikj, Etsuko N. Moriyama, Jitender S. Deogun

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

3 Scopus citations

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.

Original language	English (US)
Title of host publication	Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
Editors	Illhoi Yoo, Jane Huiru Zheng, Yang Gong, Xiaohua Tony Hu, Chi-Ren Shyu, Yana Bromberg, Jean Gao, Dmitry Korkin
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	169-174
Number of pages	6
ISBN (Electronic)	9781509030491
DOIs	https://doi.org/10.1109/BIBM.2017.8217645
State	Published - Dec 15 2017
Event	2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017 - Kansas City, United States Duration: Nov 13 2017 → Nov 16 2017

Publication series

Name	Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
Volume	2017-January

Other

Other	2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
Country/Territory	United States
City	Kansas City
Period	11/13/17 → 11/16/17

Keywords

Oxford Nanopore
Third-generation sequencing
error rates
long-read alignment
precision
recall
resources

ASJC Scopus subject areas

Biomedical Engineering
Health Informatics

Access to Document

10.1109/BIBM.2017.8217645

Cite this

Pavlovikj, N., Moriyama, E. N., & Deogun, J. S. (2017). Comparative analysis of alignment tools for nanopore reads. In I. Yoo, J. H. Zheng, Y. Gong, X. T. Hu, C.-R. Shyu, Y. Bromberg, J. Gao, & D. Korkin (Eds.), Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017 (pp. 169-174). (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; Vol. 2017-January). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM.2017.8217645

Comparative analysis of alignment tools for nanopore reads. / Pavlovikj, Natasha; Moriyama, Etsuko N.; Deogun, Jitender S.
Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. ed. / Illhoi Yoo; Jane Huiru Zheng; Yang Gong; Xiaohua Tony Hu; Chi-Ren Shyu; Yana Bromberg; Jean Gao; Dmitry Korkin. Institute of Electrical and Electronics Engineers Inc., 2017. p. 169-174 (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; Vol. 2017-January).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Pavlovikj, N, Moriyama, EN & Deogun, JS 2017, Comparative analysis of alignment tools for nanopore reads. in I Yoo, JH Zheng, Y Gong, XT Hu, C-R Shyu, Y Bromberg, J Gao & D Korkin (eds), Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017, vol. 2017-January, Institute of Electrical and Electronics Engineers Inc., pp. 169-174, 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017, Kansas City, United States, 11/13/17. https://doi.org/10.1109/BIBM.2017.8217645

Pavlovikj N, Moriyama EN, Deogun JS. Comparative analysis of alignment tools for nanopore reads. In Yoo I, Zheng JH, Gong Y, Hu XT, Shyu CR, Bromberg Y, Gao J, Korkin D, editors, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Institute of Electrical and Electronics Engineers Inc. 2017. p. 169-174. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017). doi: 10.1109/BIBM.2017.8217645

Pavlovikj, Natasha ; Moriyama, Etsuko N. ; Deogun, Jitender S. / Comparative analysis of alignment tools for nanopore reads. Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. editor / Illhoi Yoo ; Jane Huiru Zheng ; Yang Gong ; Xiaohua Tony Hu ; Chi-Ren Shyu ; Yana Bromberg ; Jean Gao ; Dmitry Korkin. Institute of Electrical and Electronics Engineers Inc., 2017. pp. 169-174 (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017).

@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.}",

note = "Publisher Copyright: {\textcopyright} 2017 IEEE.; 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017 ; Conference date: 13-11-2017 Through 16-11-2017",

year = "2017",

month = dec,

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",

}

TY - GEN

T1 - Comparative analysis of alignment tools for nanopore reads

AU - Pavlovikj, Natasha

AU - Moriyama, Etsuko N.

AU - Deogun, Jitender S.

PY - 2017/12/15

Y1 - 2017/12/15

N2 - 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.

AB - 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.

KW - Oxford Nanopore

KW - Third-generation sequencing

KW - error rates

KW - long-read alignment

KW - precision

KW - recall

KW - resources

UR - http://www.scopus.com/inward/record.url?scp=85046288627&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85046288627&partnerID=8YFLogxK

U2 - 10.1109/BIBM.2017.8217645

DO - 10.1109/BIBM.2017.8217645

M3 - Conference contribution

AN - SCOPUS:85046288627

T3 - Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017

SP - 169

EP - 174

BT - Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017

A2 - Yoo, Illhoi

A2 - Zheng, Jane Huiru

A2 - Gong, Yang

A2 - Hu, Xiaohua Tony

A2 - Shyu, Chi-Ren

A2 - Bromberg, Yana

A2 - Gao, Jean

A2 - Korkin, Dmitry

PB - Institute of Electrical and Electronics Engineers Inc.

T2 - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017

Y2 - 13 November 2017 through 16 November 2017

ER -

Comparative analysis of alignment tools for nanopore reads

Abstract

Publication series

Other

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this