|Title||Unlocking short read sequencing for metagenomics.|
|Publication Type||Journal Article|
|Year of Publication||2010|
|Authors||Rodrigue, S, Materna, AC, Timberlake, SC, Blackburn, MC, Malmstrom, RR, Alm, EJ, Chisholm, SW|
|Keywords||Metagenomics, Sequence Analysis, DNA, Software|
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.
|Alternate Journal||PLoS ONE|
|PubMed Central ID||PMC2911387|