title: Unlocking short read sequencing for metagenomics.
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.
  
  
  RESULTS
  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
  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.
authors.affiliation: Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachussetts, United States of America.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Rodrigue
authors.forename: Arne C
authors.initials: AC
authors.lastname: Materna
authors.forename: Sonia C
authors.initials: SC
authors.lastname: Timberlake
authors.forename: Matthew C
authors.initials: MC
authors.lastname: Blackburn
authors.forename: Rex R
authors.initials: RR
authors.lastname: Malmstrom
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Alm
authors.forename: Sallie W
authors.initials: SW
authors.lastname: Chisholm
mesh_terms: D056186:Metagenomics / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software