Unlocking short read sequencing for metagenomics.

• Main Authors: Sébastien Rodrigue, Arne C Materna, Sonia C Timberlake, Matthew C Blackburn, Rex R Malmstrom, Eric J Alm, Sallie W Chisholm
• Format: Article
• Language: English
• Published: Public Library of Science (PLoS) 2010-07-01
• Series: PLoS ONE
• Online Access: https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20676378/?tool=EBI

<h4>Background</h4>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.<h4>Methodology/principal findings</h4>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.<h4>Conclusions/significance</h4>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.