title: Assembling short reads from jumping libraries with large insert sizes.
abstract: BACKGROUND
  Advances in Next-Generation Sequencing technologies and sample preparation recently enabled generation of high-quality jumping libraries that have a potential to significantly improve short read assemblies. However, assembly algorithms have to catch up with experimental innovations to benefit from them and to produce high-quality assemblies.
  
  
  RESULTS
  We present a new algorithm that extends recently described exSPAnder universal repeat resolution approach to enable its applications to several challenging data types, including jumping libraries generated by the recently developed Illumina Nextera Mate Pair protocol. We demonstrate that, with these improvements, bacterial genomes often can be assembled in a few contigs using only a single Nextera Mate Pair library of short reads.
  
  
  METHODS
  Described algorithms are implemented in C++ as a part of SPAdes genome assembler, which is freely available at bioinf.spbau.ru/en/spades.
  
  
  BACKGROUND
  ap@bioinf.spbau.ru
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Algorithmic Biology Lab, St. Petersburg Academic University 194021.
authors.forename: Irina
authors.initials: I
authors.lastname: Vasilinetc
authors.affiliation: Algorithmic Biology Lab, St. Petersburg Academic University 194021, Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St.Petersburg State University, 199004.
authors.forename: Andrey D
authors.initials: AD
authors.lastname: Prjibelski
authors.affiliation: Algorithmic Biology Lab, St. Petersburg Academic University 194021, Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St.Petersburg State University, 199004.
authors.forename: Alexey
authors.initials: A
authors.lastname: Gurevich
authors.affiliation: Algorithmic Biology Lab, St. Petersburg Academic University 194021, Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St.Petersburg State University, 199004, Department of Mathematics and Mechanics, St. Petersburg State University, St. Petersburg, 198504, Russia and.
authors.forename: Anton
authors.initials: A
authors.lastname: Korobeynikov
authors.affiliation: Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St.Petersburg State University, 199004, Department of Computer Science and Engineering, University of California, San Diego, CA 92093-0404, USA.
authors.forename: Pavel A
authors.initials: PA
authors.lastname: Pevzner
mesh_terms: D000465:Algorithms; D015723:Gene Library; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods