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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:
 [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1]
  1. Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States). Dept. of Civil and Environmental Engineering
Publication Date:
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.
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. https://doi.org/10.1371/journal.pone.0011840
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. https://doi.org/10.1371/journal.pone.0011840. https://www.osti.gov/servlets/purl/1026647.
@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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Cited by: 92 works
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