BWTaligner: a genome short-read aligner
The development of next-generation sequencing technologies has helped sequence large genomes easily, producing a huge number of short-reads - small fragments of DNA. Despite the existence of many developed alignment tools, mapping short-read datasets to the reference genome, a crucial step of genom...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Vietnam Ministry of Science and Technology
2018-06-01
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| Series: | Vietnam Journal of Science, Technology and Engineering |
| Subjects: | |
| Online Access: | https://vietnamscience.vjst.vn/index.php/vjste/article/view/246 |
| _version_ | 1797937744615309312 |
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| author | Lam Nguyen Xuan Thi Trinh Hien Trinh Dang Hung Tran Cuong Nguyen |
| author_facet | Lam Nguyen Xuan Thi Trinh Hien Trinh Dang Hung Tran Cuong Nguyen |
| author_sort | Lam Nguyen |
| collection | DOAJ |
| description |
The development of next-generation sequencing technologies has helped sequence large genomes easily, producing a huge number of short-reads - small fragments of DNA. Despite the existence of many developed alignment tools, mapping short-read datasets to the reference genome, a crucial step of genome analysis, still remains a challenge. In this study, we develop a short-read alignment program, BWTaligner, based on the Burrows-Wheeler transform compression - exact and inexact matching. We tested it on the paired-end read data simulated from chromosome 9 of the rice genome to compare the alignment and single-nucleotide polymorphism (SNP) calling between our aligner and BWA - the preferred alignment program. The results showed that the BWA delivers higher recall and F-score, while BWTaligner has better precision in high coverage depth.
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| first_indexed | 2024-04-10T18:49:05Z |
| format | Article |
| id | doaj.art-3fc4c0ef726948079c3b04d1f9f8ee44 |
| institution | Directory Open Access Journal |
| issn | 2525-2461 2615-9937 |
| language | English |
| last_indexed | 2024-04-10T18:49:05Z |
| publishDate | 2018-06-01 |
| publisher | Vietnam Ministry of Science and Technology |
| record_format | Article |
| series | Vietnam Journal of Science, Technology and Engineering |
| spelling | doaj.art-3fc4c0ef726948079c3b04d1f9f8ee442023-02-01T08:20:34ZengVietnam Ministry of Science and TechnologyVietnam Journal of Science, Technology and Engineering2525-24612615-99372018-06-0160210.31276/VJSTE.60(2).73BWTaligner: a genome short-read alignerLam Nguyen0Xuan Thi Trinh1Hien Trinh2Dang Hung Tran3Cuong Nguyen4Vinmec Research Institute of Stem Cell and Gene TechnologyFaculty of Information Technology, Hanoi Open UniversityLaboratory of Genetic Engineering, Institute of Biotechnology, Vietnam Academy of Science and TechnologyHanoi National University of EducationVinmec Research Institute of Stem Cell and Gene Technology The development of next-generation sequencing technologies has helped sequence large genomes easily, producing a huge number of short-reads - small fragments of DNA. Despite the existence of many developed alignment tools, mapping short-read datasets to the reference genome, a crucial step of genome analysis, still remains a challenge. In this study, we develop a short-read alignment program, BWTaligner, based on the Burrows-Wheeler transform compression - exact and inexact matching. We tested it on the paired-end read data simulated from chromosome 9 of the rice genome to compare the alignment and single-nucleotide polymorphism (SNP) calling between our aligner and BWA - the preferred alignment program. The results showed that the BWA delivers higher recall and F-score, while BWTaligner has better precision in high coverage depth. https://vietnamscience.vjst.vn/index.php/vjste/article/view/246Burrows-Wheeler transformhigh-throughput sequencingpaired-end short readssequence alignment |
| spellingShingle | Lam Nguyen Xuan Thi Trinh Hien Trinh Dang Hung Tran Cuong Nguyen BWTaligner: a genome short-read aligner Vietnam Journal of Science, Technology and Engineering Burrows-Wheeler transform high-throughput sequencing paired-end short reads sequence alignment |
| title | BWTaligner: a genome short-read aligner |
| title_full | BWTaligner: a genome short-read aligner |
| title_fullStr | BWTaligner: a genome short-read aligner |
| title_full_unstemmed | BWTaligner: a genome short-read aligner |
| title_short | BWTaligner: a genome short-read aligner |
| title_sort | bwtaligner a genome short read aligner |
| topic | Burrows-Wheeler transform high-throughput sequencing paired-end short reads sequence alignment |
| url | https://vietnamscience.vjst.vn/index.php/vjste/article/view/246 |
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