Comparative analysis of alignment tools for application on Nanopore sequencing data
INTRODUCTION: Long-read sequencing techniques such as Oxford Nanopore sequencing, are representing a promising novel approach in molecular-biological methodology, enabling potential facilitation in mapping and de novo assembly. In comparison to conventional sequencing methods, novel alignment tools...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
De Gruyter
2021-10-01
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| Series: | Current Directions in Biomedical Engineering |
| Subjects: | |
| Online Access: | https://doi.org/10.1515/cdbme-2021-2212 |
| _version_ | 1797989285057527808 |
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| author | Becht Chiara Schmidt Jonas Blessing Frithjof Wenzel Folker |
| author_facet | Becht Chiara Schmidt Jonas Blessing Frithjof Wenzel Folker |
| author_sort | Becht Chiara |
| collection | DOAJ |
| description | INTRODUCTION: Long-read sequencing techniques such as Oxford Nanopore sequencing, are representing a promising novel approach in molecular-biological methodology, enabling potential facilitation in mapping and de novo assembly. In comparison to conventional sequencing methods, novel alignment tools are mandated to compensate differing data structures (especially high error rate) to achieve acceptably accurate analysis results. METHODS: In this study, benchmarking for long read aligners BLASR, GraphMap, LAST, minimap2, NGMLR and the short-read aligner BWA MEM on three experimental datasets was conducted. Obtained alignment results were compared for various quality and performance criteria, such as match rate, mismatch rate, error rate, working memory usage and computational time. RESULTS: The comparison yielded differences in alignment quality and performance of tools under test. Tool LAST showed the largest differences among all tools. Minimap2 achieved constant quality with good performance. BLASR, GraphMap, BWA MEM and NGMLR showed slight differences only. CONCLUSION: Differences among the tools could be reasoned with dataset characteristics and algorithm approaches of individual tools. All tools except BLASR seem applicable for Nanopore sequencing data. Therefore, selection of the tool should be done under consideration of the experimental design and the further downstream analysis |
| first_indexed | 2024-04-11T08:17:49Z |
| format | Article |
| id | doaj.art-2bc3ea5afa5d477b9a612ab5a378367b |
| institution | Directory Open Access Journal |
| issn | 2364-5504 |
| language | English |
| last_indexed | 2024-04-11T08:17:49Z |
| publishDate | 2021-10-01 |
| publisher | De Gruyter |
| record_format | Article |
| series | Current Directions in Biomedical Engineering |
| spelling | doaj.art-2bc3ea5afa5d477b9a612ab5a378367b2022-12-22T04:35:04ZengDe GruyterCurrent Directions in Biomedical Engineering2364-55042021-10-017283183410.1515/cdbme-2021-2212Comparative analysis of alignment tools for application on Nanopore sequencing dataBecht Chiara0Schmidt Jonas1Blessing Frithjof2Wenzel Folker3Faculty of Medical and Life Sciences, Hochschule Furtwangen,Schwenningen, GermanyMVZ Laborärzte Singen,Singen, GermanyMVZ Laborärzte Singen,Singen, GermanyFaculty of Medical and Life Sciences, Hochschule Furtwangen,Schwenningen, GermanyINTRODUCTION: Long-read sequencing techniques such as Oxford Nanopore sequencing, are representing a promising novel approach in molecular-biological methodology, enabling potential facilitation in mapping and de novo assembly. In comparison to conventional sequencing methods, novel alignment tools are mandated to compensate differing data structures (especially high error rate) to achieve acceptably accurate analysis results. METHODS: In this study, benchmarking for long read aligners BLASR, GraphMap, LAST, minimap2, NGMLR and the short-read aligner BWA MEM on three experimental datasets was conducted. Obtained alignment results were compared for various quality and performance criteria, such as match rate, mismatch rate, error rate, working memory usage and computational time. RESULTS: The comparison yielded differences in alignment quality and performance of tools under test. Tool LAST showed the largest differences among all tools. Minimap2 achieved constant quality with good performance. BLASR, GraphMap, BWA MEM and NGMLR showed slight differences only. CONCLUSION: Differences among the tools could be reasoned with dataset characteristics and algorithm approaches of individual tools. All tools except BLASR seem applicable for Nanopore sequencing data. Therefore, selection of the tool should be done under consideration of the experimental design and the further downstream analysishttps://doi.org/10.1515/cdbme-2021-2212alignment toolsnanopore sequencingbenchmarkingcomparative analysis |
| spellingShingle | Becht Chiara Schmidt Jonas Blessing Frithjof Wenzel Folker Comparative analysis of alignment tools for application on Nanopore sequencing data Current Directions in Biomedical Engineering alignment tools nanopore sequencing benchmarking comparative analysis |
| title | Comparative analysis of alignment tools for application on Nanopore sequencing data |
| title_full | Comparative analysis of alignment tools for application on Nanopore sequencing data |
| title_fullStr | Comparative analysis of alignment tools for application on Nanopore sequencing data |
| title_full_unstemmed | Comparative analysis of alignment tools for application on Nanopore sequencing data |
| title_short | Comparative analysis of alignment tools for application on Nanopore sequencing data |
| title_sort | comparative analysis of alignment tools for application on nanopore sequencing data |
| topic | alignment tools nanopore sequencing benchmarking comparative analysis |
| url | https://doi.org/10.1515/cdbme-2021-2212 |
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