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:
-
- 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 = {Wed Jul 28 00:00:00 EDT 2010},
month = {Wed Jul 28 00:00:00 EDT 2010}
}
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