Cited by 168Genomics and Phylogenetic StudiesEnvironmental DNA in Biodiversity StudiesMicrobial Community Ecology and Physiology

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Unlocking Short Read Sequencing for Metagenomics

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Rodrigue, Sébastien, Materna, Arne C., Timberlake, Sonia C., Blackburn, Matthew C., Malmstrom, Rex R., Alm, Eric J., Chisholm, Sallie W.·2010·PLoS ONE

DOI 10.1371/journal.pone.0011840PMC PMC2911387

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Abstract

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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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.
ORCID: Rodrigue, Sébastien
Blackburn, Matthew C.
Malmstrom, Rex R.
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)
DOI: 10.1371/journal.pone.0011840
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
Licence: cc-by
creativecommons.org/licenses/by/4.0/ (unspecified)
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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Unlocking Short Read Sequencing for Metagenomics

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