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 |
Journal | PLoS One |
Volume | 5 |
Issue | 7 |
Pagination | e11840 |
Date Published | 2010 |
ISSN | 1932-6203 |
Keywords | Metagenomics, Sequence Analysis, DNA, Software |
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. |
DOI | 10.1371/journal.pone.0011840 |
Alternate Journal | PLoS ONE |
PubMed ID | 20676378 |
PubMed Central ID | PMC2911387 |