Unlocking Short Read Sequencing for Metagenomics

doi:10.1371/journal.pone.0011840

Title: Unlocking Short Read Sequencing for Metagenomics

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}

}

Copy to clipboard

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DOI: 10.1371/journal.pone.0011840

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Cited by: 92 works

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Error filtering, pair assembly and error correction for next-generation sequencing reads
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Similar Records

Title: Unlocking Short Read Sequencing for Metagenomics

Abstract

Citation Formats

Next-generation sequencing transforms today's biology journal, December 2007

Parallel, tag-directed assembly of locally derived short sequence reads journal, January 2010

The Long March: A Sample Preparation Technique that Enhances Contig Length and Coverage by High-Throughput Short-Read Sequencing journal, October 2008

A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454 journal, January 2010

Solid-phase reversible immobilization for the isolation of PCR products journal, January 1995

DNA purification and isolation using a solid-phase journal, January 1994

Magnetic hydrophilic methacrylate-based polymer microspheres for genomic DNA isolation journal, February 2005

Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities journal, March 1998

Short clones or long clones? A simulation study on the use of paired reads in metagenomics journal, January 2010

Widespread known and novel phosphonate utilization pathways in marine bacteria revealed by functional screening and metagenomic analyses journal, January 2010

Metagenomics: Read Length Matters journal, January 2008

Gene prediction in metagenomic fragments: A large scale machine learning approach journal, April 2008

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models journal, August 2009

Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus journal, January 2007

Whole Genome Amplification and De novo Assembly of Single Bacterial Cells journal, September 2009

Accurate whole human genome sequencing using reversible terminator chemistry journal, November 2008

Amplification of cDNA ends based on template-switching effect and step- out PCR journal, March 1999

Regulation of average length of complex PCR product journal, September 1999

An improved PCR method for walking in uncloned genomic DNA journal, January 1995

Mapping short DNA sequencing reads and calling variants using mapping quality scores journal, November 2008

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs journal, September 1997

MEGAN analysis of metagenomic data journal, February 2007

Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus journal, April 2014

CREST – Classification Resources for Environmental Sequence Tags journal, November 2012

Prevention, diagnosis and treatment of high-throughput sequencing data pathologies journal, March 2014

WiseScaffolder: an algorithm for the semi-automatic scaffolding of Next Generation Sequencing data journal, September 2015

Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus journal, September 2014

Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective journal, September 2012

FLASH: fast length adjustment of short reads to improve genome assemblies journal, September 2011

COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly journal, October 2012

Error filtering, pair assembly and error correction for next-generation sequencing reads journal, July 2015

The Amazon continuum dataset: quantitative metagenomic and metatranscriptomic inventories of the Amazon River plume, June 2010 journal, January 2014

Practical guidelines for B-cell receptor repertoire sequencing analysis journal, November 2015

Optimizing Information in Next-Generation-Sequencing (NGS) Reads for Improving De Novo Genome Assembly journal, July 2013

Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus journal, September 2014

Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective journal, September 2012

FLASH: fast length adjustment of short reads to improve genome assemblies journal, September 2011

COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly journal, October 2012

Error filtering, pair assembly and error correction for next-generation sequencing reads journal, July 2015

Prevention, diagnosis and treatment of high-throughput sequencing data pathologies journal, March 2014

Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus journal, April 2014

Short-read reading-frame predictors are not created equal: sequence error causes loss of signal journal, July 2012

The Amazon continuum dataset: quantitative metagenomic and metatranscriptomic inventories of the Amazon River plume, June 2010 journal, January 2014

WiseScaffolder: an algorithm for the semi-automatic scaffolding of Next Generation Sequencing data journal, September 2015

Practical guidelines for B-cell receptor repertoire sequencing analysis journal, November 2015

Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance journal, October 2012

CREST – Classification Resources for Environmental Sequence Tags journal, November 2012

Optimizing Information in Next-Generation-Sequencing (NGS) Reads for Improving De Novo Genome Assembly journal, July 2013

PEAR: a fast and accurate Illumina Paired-End reAd mergeR journal, October 2013

First draft genome sequence of a strain belonging to the Zoogloea genus and its gene expression in situ journal, October 2017

Next-generation sequencing transforms today's biology
journal, December 2007

Parallel, tag-directed assembly of locally derived short sequence reads
journal, January 2010

The Long March: A Sample Preparation Technique that Enhances Contig Length and Coverage by High-Throughput Short-Read Sequencing
journal, October 2008

A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454
journal, January 2010

Solid-phase reversible immobilization for the isolation of PCR products
journal, January 1995

DNA purification and isolation using a solid-phase
journal, January 1994

Magnetic hydrophilic methacrylate-based polymer microspheres for genomic DNA isolation
journal, February 2005

Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
journal, March 1998

Short clones or long clones? A simulation study on the use of paired reads in metagenomics
journal, January 2010

Widespread known and novel phosphonate utilization pathways in marine bacteria revealed by functional screening and metagenomic analyses
journal, January 2010

Metagenomics: Read Length Matters
journal, January 2008

Gene prediction in metagenomic fragments: A large scale machine learning approach
journal, April 2008

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models
journal, August 2009

Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus
journal, January 2007

Whole Genome Amplification and De novo Assembly of Single Bacterial Cells
journal, September 2009

Accurate whole human genome sequencing using reversible terminator chemistry
journal, November 2008

Amplification of cDNA ends based on template-switching effect and step- out PCR
journal, March 1999

Regulation of average length of complex PCR product
journal, September 1999

An improved PCR method for walking in uncloned genomic DNA
journal, January 1995

Mapping short DNA sequencing reads and calling variants using mapping quality scores
journal, November 2008

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
journal, September 1997

MEGAN analysis of metagenomic data
journal, February 2007

Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus
journal, April 2014

CREST – Classification Resources for Environmental Sequence Tags
journal, November 2012

Prevention, diagnosis and treatment of high-throughput sequencing data pathologies
journal, March 2014

WiseScaffolder: an algorithm for the semi-automatic scaffolding of Next Generation Sequencing data
journal, September 2015

Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus
journal, September 2014

Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective
journal, September 2012

FLASH: fast length adjustment of short reads to improve genome assemblies
journal, September 2011

COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
journal, October 2012

Error filtering, pair assembly and error correction for next-generation sequencing reads
journal, July 2015

The Amazon continuum dataset: quantitative metagenomic and metatranscriptomic inventories of the Amazon River plume, June 2010
journal, January 2014

Practical guidelines for B-cell receptor repertoire sequencing analysis
journal, November 2015

Optimizing Information in Next-Generation-Sequencing (NGS) Reads for Improving De Novo Genome Assembly
journal, July 2013

Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus
journal, September 2014

Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective
journal, September 2012

FLASH: fast length adjustment of short reads to improve genome assemblies
journal, September 2011

COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
journal, October 2012

Error filtering, pair assembly and error correction for next-generation sequencing reads
journal, July 2015

Prevention, diagnosis and treatment of high-throughput sequencing data pathologies
journal, March 2014

Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus
journal, April 2014

Short-read reading-frame predictors are not created equal: sequence error causes loss of signal
journal, July 2012

The Amazon continuum dataset: quantitative metagenomic and metatranscriptomic inventories of the Amazon River plume, June 2010
journal, January 2014

WiseScaffolder: an algorithm for the semi-automatic scaffolding of Next Generation Sequencing data
journal, September 2015

Practical guidelines for B-cell receptor repertoire sequencing analysis
journal, November 2015

Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance
journal, October 2012

CREST – Classification Resources for Environmental Sequence Tags
journal, November 2012

Optimizing Information in Next-Generation-Sequencing (NGS) Reads for Improving De Novo Genome Assembly
journal, July 2013

PEAR: a fast and accurate Illumina Paired-End reAd mergeR
journal, October 2013

First draft genome sequence of a strain belonging to the Zoogloea genus and its gene expression in situ
journal, October 2017