title: De novo finished 2.8 Mbp Staphylococcus aureus genome assembly from 100 bp short and long range paired-end reads.
abstract: BACKGROUND
  Paired-end sequencing allows circumventing the shortness of the reads produced by second generation sequencers and is essential for de novo assembly of genomes. However, obtaining a finished genome from short reads is still an open challenge. We present an algorithm that exploits the pairing information issued from inserts of potentially any length. The method determines paths through an overlaps graph by using a constrained search tree. We also present a method that automatically determines suited overlaps cutoffs according to the contextual coverage, reducing thus the need for manual parameterization. Finally, we introduce an interactive mode that allows querying an assembly at targeted regions.
  
  
  RESULTS
  We assess our methods by assembling two Staphylococcus aureus strains that were sequenced on the Illumina platform. Using 100 bp paired-end reads and minimal manual curation, we produce a finished genome sequence for the previously undescribed isolate SGH-10-168.
  
  
  METHODS
  The presented algorithms are implemented in the standalone Edena software, freely available under the General Public License (GPLv3) at www.genomic.ch/edena.php.
authors.affiliation: Genomic Research Laboratory, Infectious Diseases Service, Geneva University Hospitals, 1211 Geneva 4, Switzerland, Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, USA, BioMérieux, Data and Knowledge Laboratory, 69280 Marcy l'Etoile, France and Fasteris SA, PO Box 28, 1228 Plan-les-Ouates, Switzerland.
authors.forename: David
authors.initials: D
authors.lastname: Hernandez
authors.forename: Ryan
authors.initials: R
authors.lastname: Tewhey
authors.forename: Jean-Baptiste
authors.initials: JB
authors.lastname: Veyrieras
authors.forename: Laurent
authors.initials: L
authors.lastname: Farinelli
authors.forename: Magne
authors.initials: M
authors.lastname: Østerås
authors.forename: Patrice
authors.initials: P
authors.lastname: François
authors.forename: Jacques
authors.initials: J
authors.lastname: Schrenzel
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D016678:Genome; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software; D013211:Staphylococcus aureus / Q000235:genetics*