Unlocking Short Read Sequencing for Metagenomics

doi:10.1371/journal.pone.0011840

Title: Unlocking Short Read Sequencing for Metagenomics

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Abstract

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.

Authors:

Rodrigue, Sébastien ^[1]; Materna, Arne C. ^[1]; Timberlake, Sonia C. ^[1]; Blackburn, Matthew C. ^[1]; Malmstrom, Rex R. ^[1]; Alm, Eric J. ^[1]; Chisholm, Sallie W. ^[1]; Gilbert, Jack Anthony ^[1]

Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States). Dept. of Civil and Environmental Engineering

Publication Date:: 2010-07-28

Research Org.:: Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)

Sponsoring Org.:: USDOE

OSTI Identifier:: 1026647

Report Number(s):: DoE/ER/-64506-4
Journal ID: ISSN 1932-6203

Grant/Contract Number:: FG02-07ER64506

Resource Type:: Accepted Manuscript

Journal Name:: PLoS ONE

Additional Journal Information:: Journal Volume: 5; Journal Issue: 7; Journal ID: ISSN 1932-6203

Publisher:: Public Library of Science

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES

Citation Formats


                    Rodrigue, Sébastien, Materna, Arne C., Timberlake, Sonia C., Blackburn, Matthew C., Malmstrom, Rex R., Alm, Eric J., Chisholm, Sallie W., and Gilbert, Jack Anthony. Unlocking Short Read Sequencing for Metagenomics.  United States: N. p., 2010. 
        Web.  doi:10.1371/journal.pone.0011840.

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                    Rodrigue, Sébastien, Materna, Arne C., Timberlake, Sonia C., Blackburn, Matthew C., Malmstrom, Rex R., Alm, Eric J., Chisholm, Sallie W., & Gilbert, Jack Anthony. Unlocking Short Read Sequencing for Metagenomics.  United States.  doi:10.1371/journal.pone.0011840.

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                    Rodrigue, Sébastien, Materna, Arne C., Timberlake, Sonia C., Blackburn, Matthew C., Malmstrom, Rex R., Alm, Eric J., Chisholm, Sallie W., and Gilbert, Jack Anthony. Wed .  
        "Unlocking Short Read Sequencing for Metagenomics".  United States.  doi:10.1371/journal.pone.0011840.  https://www.osti.gov/servlets/purl/1026647.

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@article{osti_1026647,

  title        = {Unlocking Short Read Sequencing for Metagenomics},

  author       = {Rodrigue, Sébastien and Materna, Arne C. and Timberlake, Sonia C. and Blackburn, Matthew C. and Malmstrom, Rex R. and Alm, Eric J. and Chisholm, Sallie W. and Gilbert, Jack Anthony},

  abstractNote = {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.},

  doi          = {10.1371/journal.pone.0011840},

  journal      = {PLoS ONE},

  number       = 7,

  volume       = 5,

  place        = {United States},

  year         = {2010},

  month        = {7}

}

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DOI: 10.1371/journal.pone.0011840

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