Unlocking short read sequencing for metagenomics

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. We describe an experimental and computational pipeline yielding millions of rea...

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Bibliographic Details
Published in:PloS one 2010-07, Vol.5 (7), p.e11840-e11840
Main Authors: Rodrigue, Sébastien, Materna, Arne C, Timberlake, Sonia C, Blackburn, Matthew C, Malmstrom, Rex R, Alm, Eric J, Chisholm, Sallie W
Format: Article
Language:English
Subjects:
Analysis
Artificial intelligence
BASIC BIOLOGICAL SCIENCES
Biochemistry/Bioinformatics
Biotechnology
Composite materials
Computational Biology/Metagenomics
Computer applications
Deoxyribonucleic acid
DNA
DNA sequencing
Engineering
Environmental engineering
Error analysis
Genetics and Genomics
Genetics and Genomics/Bioinformatics
Genomes
Genomics
Inserts
Metagenomics - methods
Molecular Biology
Next-generation sequencing
Nucleic acids
Phylogenetics
Polyethylene glycol
Prochlorococcus
Sequence Analysis, DNA - methods
Software
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Summary: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. 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. 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.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0011840