RECORD: Reference-Assisted Genome Assembly for Closely Related Genomes
Background. Next-generation sequencing technologies are now producing multiple times the genome size in total reads from a single experiment. This is enough information to reconstruct at least some of the differences between the individual genome studied in the experiment and the reference genome of...
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| Format: | Article |
| Language: | English |
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Wiley
2015-01-01
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| Series: | International Journal of Genomics |
| Online Access: | http://dx.doi.org/10.1155/2015/563482 |
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| _version_ | 1849410235153776640 |
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| author | Krisztian Buza Bartek Wilczynski Norbert Dojer |
| author_facet | Krisztian Buza Bartek Wilczynski Norbert Dojer |
| author_sort | Krisztian Buza |
| collection | DOAJ |
| description | Background. Next-generation sequencing technologies are now producing multiple times the genome size in total reads from a single experiment. This is enough information to reconstruct at least some of the differences between the individual genome studied in the experiment and the reference genome of the species. However, in most typical protocols, this information is disregarded and the reference genome is used. Results. We provide a new approach that allows researchers to reconstruct genomes very closely related to the reference genome (e.g., mutants of the same species) directly from the reads used in the experiment. Our approach applies de novo assembly software to experimental reads and so-called pseudoreads and uses the resulting contigs to generate a modified reference sequence. In this way, it can very quickly, and at no additional sequencing cost, generate new, modified reference sequence that is closer to the actual sequenced genome and has a full coverage. In this paper, we describe our approach and test its implementation called RECORD. We evaluate RECORD on both simulated and real data. We made our software publicly available on sourceforge. Conclusion. Our tests show that on closely related sequences RECORD outperforms more general assisted-assembly software. |
| format | Article |
| id | doaj-art-78e3fa63cbd04c82ae6ed7397497c1ef |
| institution | Kabale University |
| issn | 2314-436X 2314-4378 |
| language | English |
| publishDate | 2015-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | International Journal of Genomics |
| spelling | doaj-art-78e3fa63cbd04c82ae6ed7397497c1ef2025-08-20T03:35:11ZengWileyInternational Journal of Genomics2314-436X2314-43782015-01-01201510.1155/2015/563482563482RECORD: Reference-Assisted Genome Assembly for Closely Related GenomesKrisztian Buza0Bartek Wilczynski1Norbert Dojer2Faculty of Mathematics, Informatics and Mechanics (MIM), University of Warsaw, Banacha 2, 02-097 Warsaw, PolandFaculty of Mathematics, Informatics and Mechanics (MIM), University of Warsaw, Banacha 2, 02-097 Warsaw, PolandFaculty of Mathematics, Informatics and Mechanics (MIM), University of Warsaw, Banacha 2, 02-097 Warsaw, PolandBackground. Next-generation sequencing technologies are now producing multiple times the genome size in total reads from a single experiment. This is enough information to reconstruct at least some of the differences between the individual genome studied in the experiment and the reference genome of the species. However, in most typical protocols, this information is disregarded and the reference genome is used. Results. We provide a new approach that allows researchers to reconstruct genomes very closely related to the reference genome (e.g., mutants of the same species) directly from the reads used in the experiment. Our approach applies de novo assembly software to experimental reads and so-called pseudoreads and uses the resulting contigs to generate a modified reference sequence. In this way, it can very quickly, and at no additional sequencing cost, generate new, modified reference sequence that is closer to the actual sequenced genome and has a full coverage. In this paper, we describe our approach and test its implementation called RECORD. We evaluate RECORD on both simulated and real data. We made our software publicly available on sourceforge. Conclusion. Our tests show that on closely related sequences RECORD outperforms more general assisted-assembly software.http://dx.doi.org/10.1155/2015/563482 |
| spellingShingle | Krisztian Buza Bartek Wilczynski Norbert Dojer RECORD: Reference-Assisted Genome Assembly for Closely Related Genomes International Journal of Genomics |
| title | RECORD: Reference-Assisted Genome Assembly for Closely Related Genomes |
| title_full | RECORD: Reference-Assisted Genome Assembly for Closely Related Genomes |
| title_fullStr | RECORD: Reference-Assisted Genome Assembly for Closely Related Genomes |
| title_full_unstemmed | RECORD: Reference-Assisted Genome Assembly for Closely Related Genomes |
| title_short | RECORD: Reference-Assisted Genome Assembly for Closely Related Genomes |
| title_sort | record reference assisted genome assembly for closely related genomes |
| url | http://dx.doi.org/10.1155/2015/563482 |
| work_keys_str_mv | AT krisztianbuza recordreferenceassistedgenomeassemblyforcloselyrelatedgenomes AT bartekwilczynski recordreferenceassistedgenomeassemblyforcloselyrelatedgenomes AT norbertdojer recordreferenceassistedgenomeassemblyforcloselyrelatedgenomes |