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PLoS One. 2010 Jul 28;5(7):e11840. doi: 10.1371/journal.pone.0011840.

Unlocking short read sequencing for metagenomics.

Author information

  • 1Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachussetts, United States of America.

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.

PMID:
20676378
[PubMed - indexed for MEDLINE]
PMCID:
PMC2911387
Free PMC Article

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