Annotated bacterial chromosomes from frame-shift-corrected long-read metagenomic data
Background : Short-read sequencing technologies have long been the work-horse of microbiome analysis. Continuing technological advances are making the application of long-read sequencing to metagenomic samples increasingly feasible. Results : We demonstrate that whole bacterial chromosomes can be ob...
| Main Authors: | , , , , , , , , |
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| Format: | Journal Article |
| Language: | English |
| Published: |
2019
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| Online Access: | https://hdl.handle.net/10356/106705 http://hdl.handle.net/10220/49039 |
| _version_ | 1824456181850046464 |
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| author | Arumugam, Krithika Bağcı, Caner Bessarab, Irina Beier, Sina Buchfink, Benjamin Górska, Anna Qiu, Guanglei Huson, Daniel H. Williams, Rohan B. H. |
| author2 | Singapore Centre for Environmental Life Sciences and Engineering |
| author_facet | Singapore Centre for Environmental Life Sciences and Engineering Arumugam, Krithika Bağcı, Caner Bessarab, Irina Beier, Sina Buchfink, Benjamin Górska, Anna Qiu, Guanglei Huson, Daniel H. Williams, Rohan B. H. |
| author_sort | Arumugam, Krithika |
| collection | NTU |
| description | Background : Short-read sequencing technologies have long been the work-horse of microbiome analysis. Continuing technological advances are making the application of long-read sequencing to metagenomic samples increasingly feasible. Results : We demonstrate that whole bacterial chromosomes can be obtained from an enriched community, by application of MinION sequencing to a sample from an EBPR bioreactor, producing 6 Gb of sequence that assembles into multiple closed bacterial chromosomes. We provide a simple pipeline for processing such data, which includes a new approach to correcting erroneous frame-shifts. Conclusions : Advances in long-read sequencing technology and corresponding algorithms will allow the routine extraction of whole chromosomes from environmental samples, providing a more detailed picture of individual members of a microbiome. |
| first_indexed | 2025-02-19T03:50:02Z |
| format | Journal Article |
| id | ntu-10356/106705 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2025-02-19T03:50:02Z |
| publishDate | 2019 |
| record_format | dspace |
| spelling | ntu-10356/1067052020-09-21T11:36:12Z Annotated bacterial chromosomes from frame-shift-corrected long-read metagenomic data Arumugam, Krithika Bağcı, Caner Bessarab, Irina Beier, Sina Buchfink, Benjamin Górska, Anna Qiu, Guanglei Huson, Daniel H. Williams, Rohan B. H. Singapore Centre for Environmental Life Sciences and Engineering Microbiome DRNTU::Engineering::Environmental engineering Long-read Sequencing Background : Short-read sequencing technologies have long been the work-horse of microbiome analysis. Continuing technological advances are making the application of long-read sequencing to metagenomic samples increasingly feasible. Results : We demonstrate that whole bacterial chromosomes can be obtained from an enriched community, by application of MinION sequencing to a sample from an EBPR bioreactor, producing 6 Gb of sequence that assembles into multiple closed bacterial chromosomes. We provide a simple pipeline for processing such data, which includes a new approach to correcting erroneous frame-shifts. Conclusions : Advances in long-read sequencing technology and corresponding algorithms will allow the routine extraction of whole chromosomes from environmental samples, providing a more detailed picture of individual members of a microbiome. NRF (Natl Research Foundation, S’pore) MOE (Min. of Education, S’pore) Published version 2019-07-01T04:14:48Z 2019-12-06T22:16:32Z 2019-07-01T04:14:48Z 2019-12-06T22:16:32Z 2019 Journal Article Arumugam, K., Bağcı, C., Bessarab, I., Beier, S., Buchfink, B., Górska, A., . . . Williams, R. B. H. (2019). Annotated bacterial chromosomes from frame-shift-corrected long-read metagenomic data. Microbiome, 7(1), 61-. doi:10.1186/s40168-019-0665-y https://hdl.handle.net/10356/106705 http://hdl.handle.net/10220/49039 10.1186/s40168-019-0665-y en Microbiome © 2019 The Author(s). This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. 13 p. application/pdf |
| spellingShingle | Microbiome DRNTU::Engineering::Environmental engineering Long-read Sequencing Arumugam, Krithika Bağcı, Caner Bessarab, Irina Beier, Sina Buchfink, Benjamin Górska, Anna Qiu, Guanglei Huson, Daniel H. Williams, Rohan B. H. Annotated bacterial chromosomes from frame-shift-corrected long-read metagenomic data |
| title | Annotated bacterial chromosomes from frame-shift-corrected long-read metagenomic data |
| title_full | Annotated bacterial chromosomes from frame-shift-corrected long-read metagenomic data |
| title_fullStr | Annotated bacterial chromosomes from frame-shift-corrected long-read metagenomic data |
| title_full_unstemmed | Annotated bacterial chromosomes from frame-shift-corrected long-read metagenomic data |
| title_short | Annotated bacterial chromosomes from frame-shift-corrected long-read metagenomic data |
| title_sort | annotated bacterial chromosomes from frame shift corrected long read metagenomic data |
| topic | Microbiome DRNTU::Engineering::Environmental engineering Long-read Sequencing |
| url | https://hdl.handle.net/10356/106705 http://hdl.handle.net/10220/49039 |
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