Unlocking Short Read Sequencing for Metagenomics
Background Different high-throughput nucleic acid sequencing platforms are currently available but a trade-off currently exists between the cost and number of reads that can be generated versus the read length that can be achieved. Methodology/Principal Findings We describe an experimental an...
| Main Authors: | , , , , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | en_US |
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Public Library of Science
2010
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| Online Access: | http://hdl.handle.net/1721.1/60369 https://orcid.org/0000-0001-8294-9364 |
| _version_ | 1826206270188683264 |
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| author | Chisholm, Sallie (Penny) Rodrigue, Sebastien Materna, Arne Timberlake, Sonia Crago Blackburn, Matthew C. Malmstrom, Rex R. Alm, Eric J. |
| author2 | Massachusetts Institute of Technology. Department of Biological Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Biological Engineering Chisholm, Sallie (Penny) Rodrigue, Sebastien Materna, Arne Timberlake, Sonia Crago Blackburn, Matthew C. Malmstrom, Rex R. Alm, Eric J. |
| author_sort | Chisholm, Sallie (Penny) |
| collection | MIT |
| description | Background
Different high-throughput nucleic acid sequencing platforms are currently available but a trade-off currently exists between the cost and number of reads that can be generated versus the read length that can be achieved.
Methodology/Principal Findings
We describe an experimental and computational pipeline yielding millions of reads that can exceed 200 bp with quality scores approaching that of traditional Sanger sequencing. The method combines an automatable gel-less library construction step with paired-end sequencing on a short-read instrument. With appropriately sized library inserts, mate-pair sequences can overlap, and we describe the SHERA software package that joins them to form a longer composite read.
Conclusions/Significance
This strategy is broadly applicable to sequencing applications that benefit from low-cost high-throughput sequencing, but require longer read lengths. We demonstrate that our approach enables metagenomic analyses using the Illumina Genome Analyzer, with low error rates, and at a fraction of the cost of pyrosequencing. |
| first_indexed | 2024-09-23T13:26:47Z |
| format | Article |
| id | mit-1721.1/60369 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T13:26:47Z |
| publishDate | 2010 |
| publisher | Public Library of Science |
| record_format | dspace |
| spelling | mit-1721.1/603692022-09-28T14:17:51Z Unlocking Short Read Sequencing for Metagenomics Chisholm, Sallie (Penny) Rodrigue, Sebastien Materna, Arne Timberlake, Sonia Crago Blackburn, Matthew C. Malmstrom, Rex R. Alm, Eric J. Massachusetts Institute of Technology. Department of Biological Engineering Massachusetts Institute of Technology. Department of Civil and Environmental Engineering Chisholm, Sallie (Penny) Chisholm, Sallie (Penny) Rodrigue, Sebastien Materna, Arne Timberlake, Sonia Crago Blackburn, Matthew C. Malmstrom, Rex R. Alm, Eric J. Background Different high-throughput nucleic acid sequencing platforms are currently available but a trade-off currently exists between the cost and number of reads that can be generated versus the read length that can be achieved. Methodology/Principal Findings We describe an experimental and computational pipeline yielding millions of reads that can exceed 200 bp with quality scores approaching that of traditional Sanger sequencing. The method combines an automatable gel-less library construction step with paired-end sequencing on a short-read instrument. With appropriately sized library inserts, mate-pair sequences can overlap, and we describe the SHERA software package that joins them to form a longer composite read. Conclusions/Significance This strategy is broadly applicable to sequencing applications that benefit from low-cost high-throughput sequencing, but require longer read lengths. We demonstrate that our approach enables metagenomic analyses using the Illumina Genome Analyzer, with low error rates, and at a fraction of the cost of pyrosequencing. Gordon and Betty Moore Foundation (Marine Microbiology Initiative) Center for Microbial Oceanography: Research and Education United States. Dept. of Energy (Genome-to-Life) Natural Sciences and Engineering Research Council of Canada Fonds québécois de la recherche sur la nature et les technologies 2010-12-22T20:22:59Z 2010-12-22T20:22:59Z 2010-07 2010-05 Article http://purl.org/eprint/type/JournalArticle 1932-6203 http://hdl.handle.net/1721.1/60369 Rodrigue, Sébastien et al. “Unlocking Short Read Sequencing for Metagenomics.” PLoS ONE 5.7 (2010): e11840. https://orcid.org/0000-0001-8294-9364 en_US http://dx.doi.org/10.1371/journal.pone.0011840 PLoS ONE Creative Commons Attribution http://creativecommons.org/licenses/by/2.5/ application/pdf Public Library of Science PLoS |
| spellingShingle | Chisholm, Sallie (Penny) Rodrigue, Sebastien Materna, Arne Timberlake, Sonia Crago Blackburn, Matthew C. Malmstrom, Rex R. Alm, Eric J. Unlocking Short Read Sequencing for Metagenomics |
| title | Unlocking Short Read Sequencing for Metagenomics |
| title_full | Unlocking Short Read Sequencing for Metagenomics |
| title_fullStr | Unlocking Short Read Sequencing for Metagenomics |
| title_full_unstemmed | Unlocking Short Read Sequencing for Metagenomics |
| title_short | Unlocking Short Read Sequencing for Metagenomics |
| title_sort | unlocking short read sequencing for metagenomics |
| url | http://hdl.handle.net/1721.1/60369 https://orcid.org/0000-0001-8294-9364 |
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