title: High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies.
abstract: BACKGROUND
  Massively parallel DNA sequencing instruments are enabling the decoding of whole genomes at significantly lower cost and higher throughput than classical Sanger technology. Each of these technologies have been estimated to yield assemblies with more problematic features than the standard method. These problems are of a different nature depending on the techniques used. So, an appropriate mix of technologies may help resolve most difficulties, and eventually provide assemblies of high quality without requiring any Sanger-based input.
  
  
  RESULTS
  We compared assemblies obtained using Sanger data with those from different inputs from New Sequencing Technologies. The assemblies were systematically compared with a reference finished sequence. We found that the 454 GSFLX can efficiently produce high continuity when used at high coverage. The potential to enhance continuity by scaffolding was tested using 454 sequences from circularized genomic fragments. Finally, we explore the use of Solexa-Illumina short reads to polish the genome draft by implementing a technique to correct 454 consensus errors.
  
  
  CONCLUSIONS
  High quality drafts can be produced for small genomes without any Sanger data input. We found that 454 GSFLX and Solexa/Illumina show great complementarity in producing large contigs and supercontigs with a low error rate.
authors.affiliation: CEA, DSV, Institut de Génomique, Genoscope, Evry, France. jmaury@genoscope.cns.fr
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Aury
authors.forename: Corinne
authors.initials: C
authors.lastname: Cruaud
authors.forename: Valérie
authors.initials: V
authors.lastname: Barbe
authors.forename: Odile
authors.initials: O
authors.lastname: Rogier
authors.forename: Sophie
authors.initials: S
authors.lastname: Mangenot
authors.forename: Gaelle
authors.initials: G
authors.lastname: Samson
authors.forename: Julie
authors.initials: J
authors.lastname: Poulain
authors.forename: Véronique
authors.initials: V
authors.lastname: Anthouard
authors.forename: Claude
authors.initials: C
authors.lastname: Scarpelli
authors.forename: François
authors.initials: F
authors.lastname: Artiguenave
authors.forename: Patrick
authors.initials: P
authors.lastname: Wincker
mesh_terms: D019295:Computational Biology / Q000379:methods; D020451:Contig Mapping; D015723:Gene Library; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000295:instrumentation / Q000379:methods*