The DOI matches its Crossref record; 23 of the 24 references it cites were found in a registry or an index.
Unlocking Short Read Sequencing for Metagenomics
Open accessAbstract
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.
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“Shera merges the reads by maximizing the number of matches between the paired-end reads.”
From PEAR: a fast and accurate Illumina Paired-End reAd mergeR (2014) · cites this paper as Rodrigue et al., 2010
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“Both, Shera and FLASH (see later in the text) ignore the quality scores of the base calls.”
From PEAR: a fast and accurate Illumina Paired-End reAd mergeR (2014) · cites this paper as Rodrigue et al., 2010
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“Shera merges all reads and leaves it to the user to decide which merged reads are correct.”
From PEAR: a fast and accurate Illumina Paired-End reAd mergeR (2014) · cites this paper as Rodrigue et al., 2010
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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy AssessmentPreprint
Ewing, B., Hillier, L., Wendl, M. C., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.175 · Cited by 6,993
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
Ewing, B., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.186 · Cited by 5,439
Accurate whole human genome sequencing using reversible terminator chemistry
Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., Brown, C. G., Hall, K. P., Evers, D. J., Barnes, C. L., Bignell, H. R., et al. (2008) · Nature · doi:10.1038/nature07517 · Cited by 3,684
MEGAN analysis of metagenomic dataPreprint
Huson, D. H., Auch, A. F., Qi, J., & Schuster, S. C. (2007) · Genome Research · doi:10.1101/gr.5969107 · Cited by 3,294
Mapping short DNA sequencing reads and calling variants using mapping quality scores
Li, H., Ruan, J., & Durbin, R. (2008) · Genome Research · doi:10.1101/gr.078212.108 · Cited by 2,638
Next-generation sequencing transforms today's biology
Schuster, S. C. (2007) · Nature Methods · doi:10.1038/nmeth1156 · Cited by 1,870
An improved PCR method for walking in uncloned genomic DNA
Siebert, P. D., Chenchik, A. A., Kellogg, D. E., Lukyanov, K. A., & Lukyanov, S. (1995) · Nucleic Acids Research · doi:10.1093/nar/23.6.1087 · Cited by 1,014
Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus
Kettler, G. C., Martiny, A. C., Huang, K. H., Zucker, J., Coleman, M. L., Rodrigue, S., Chen, F., Lapidus, A. L., Ferriera, S., Johnson, J. H., et al. (2007) · PLoS Genetics · doi:10.1371/journal.pgen.0030231 · Cited by 552
Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models
Brady, A., & Salzberg, S. L. (2009) · Nature Methods · doi:10.1038/nmeth.1358 · Cited by 526
Solid-phase reversible immobilization for the isolation of PCR products
DeAngelis, M. M., Wang, D. G., & Hawkins, T. L. (1995) · Nucleic Acids Research · doi:10.1093/nar/23.22.4742 · Cited by 393
Amplification of cDNA ends based on template-switching effect and step- out PCR
Matz, M. V. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.6.1558 · Cited by 380
Metagenomics: Read Length Matters
Wommack, K. E., Bhavsar, J., & Ravel, J. (2008) · Applied and Environmental Microbiology · doi:10.1128/aem.02181-07 · Cited by 331
Whole Genome Amplification and De novo Assembly of Single Bacterial Cells
Rodrigue, S., Malmstrom, R. R., Berlin, A. M., Birren, B. W., Henn, M. R., & Chisholm, S. W. (2009) · PLoS ONE · doi:10.1371/journal.pone.0006864 · Cited by 259
DNA purification and isolation using a solid-phase
Hawkins, T. L., O‘Connor-Morin, T., Roy, A., & Santillan, C. (1994) · Nucleic Acids Research · doi:10.1093/nar/22.21.4543 · Cited by 227
Martinez, A., Tyson, G. W., & DeLong, E. F. (2009) · Environmental Microbiology · doi:10.1111/j.1462-2920.2009.02062.x · Cited by 209
Parallel, tag-directed assembly of locally derived short sequence reads
Hiatt, J. B., Patwardhan, R. P., Turner, E. H., Lee, C., & Shendure, J. (2010) · Nature Methods · doi:10.1038/nmeth.1416 · Cited by 149
Gene prediction in metagenomic fragments: A large scale machine learning approach
Hoff, K. J., Tech, M., Lingner, T., Daniel, R., Morgenstern, B., & Meinicke, P. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-217 · Cited by 109
A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454
Lennon, N. J., Lintner, R. E., Anderson, S. T., Alvarez, P. A., Barry, A. J., Brockman, W., Daza, R. M., Erlich, R., Giannoukos, G., Green, L., et al. (2010) · Genome biology · doi:10.1186/gb-2010-11-2-r15 · Cited by 107
Magnetic hydrophilic methacrylate-based polymer microspheres for genomic DNA isolation
Křížová, J., Španová, A., Rittich, B., & Horák, D. (2005) · Journal of Chromatography A · doi:10.1016/j.chroma.2004.12.014 · Cited by 89
Regulation of average length of complex PCR product
Shagin, D. A. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.18.e23 · Cited by 73
Sorber, K., Chiu, C. Y., Webster, D. R., Dimon, M. T., Ruby, J. G., Hekele, A., & DeRisi, J. L. (2008) · PLoS ONE · doi:10.1371/journal.pone.0003495 · Cited by 29
Short clones or long clones? A simulation study on the use of paired reads in metagenomics
Mitra, S., Schubach, M., & Huson, D. H. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-s1-s12 · Cited by 22
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1 of the 24 references couldn’t be matched to a known paper.
Cited by
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FLASH: fast length adjustment of short reads to improve genome assemblies
Magoč, T., & Salzberg, S. L. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr507 · Cited by 15,366
PEAR: a fast and accurate Illumina Paired-End reAd mergeR
Zhang, J., Kobert, K., Flouri, T., & Stamatakis, A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btt593 · Cited by 4,497
PANDAseq: paired-end assembler for Illumina sequences
Masella, A. P., Bartram, A. K., Truszkowski, J. M., Brown, D. G., & Neufeld, J. D. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-31 · Cited by 2,132
Error filtering, pair assembly and error correction for next-generation sequencing reads
Edgar, R. C., & Flyvbjerg, H. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv401 · Cited by 1,315
Next-generation transcriptome assembly
Martin, J. A., & Wang, Z. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3068 · Cited by 1,309
Metadata
- Authors
- Rodrigue, S., Materna, A. C., Timberlake, S. C., Blackburn, M. C., Malmstrom, R. R., Alm, E. J., & Chisholm, S. W.
- Affiliations
- Massachusetts Institute of Technology (US)
- Corresponding author
- Alm, Eric J.
- Chisholm, Sallie W.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2010-07-28
- Volume
- 5
- Issue
- 7
- Pages
- e11840
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC2911387
- OpenAlex
- W2151671981
- Cited by
- 168
- References
- 24
- Citations by year
- 2025: 5 · 2024: 2 · 2023: 6 · 2022: 2 · 2021: 1 · 2020: 6 · 2019: 3 · 2018: 10 · 2017: 7 · 2016: 13 · 2015: 21 · 2014: 32 · 2013: 29 · 2012: 16
- FWCI
- 7.56
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS ONE (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
- Figshare (submittedVersion, cc-by)
- Funders
- U.S. Department of Energy (DEFG0207ER64506)
- Gordon and Betty Moore Foundation
- Fonds Québécois de la Recherche sur la Nature et les Technologies
- Natural Sciences and Engineering Research Council of Canada
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Environmental Science › Ecology › Environmental DNA in Biodiversity Studies
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- metagenomics, short-read sequencing, long-read sequencing, paired-end sequencing, sequencing cost, read length
- MeSH terms
- Software, Sequence Analysis, DNA, Metagenomics
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