title: ExSPAnder: a universal repeat resolver for DNA fragment assembly.
abstract: Next-generation sequencing (NGS) technologies have raised a challenging de novo genome assembly problem that is further amplified in recently emerged single-cell sequencing projects. While various NGS assemblers can use information from several libraries of read-pairs, most of them were originally developed for a single library and do not fully benefit from multiple libraries. Moreover, most assemblers assume uniform read coverage, condition that does not hold for single-cell projects where utilization of read-pairs is even more challenging. We have developed an exSPAnder algorithm that accurately resolves repeats in the case of both single and multiple libraries of read-pairs in both standard and single-cell assembly projects.
  
  
  METHODS
  http://bioinf.spbau.ru/en/spades
authors.affiliation: Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia, Department of Mathematics and Mechanics, Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia and Department of Computer Science and Engineering, University of California, San Diego, USA.
authors.forename: Andrey D
authors.initials: AD
authors.lastname: Prjibelski
authors.affiliation: Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia, Department of Mathematics and Mechanics, Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia and Department of Computer Science and Engineering, University of California, San Diego, USA.
authors.forename: Irina
authors.initials: I
authors.lastname: Vasilinetc
authors.affiliation: Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia, Department of Mathematics and Mechanics, Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia and Department of Computer Science and Engineering, University of California, San Diego, USA.
authors.forename: Anton
authors.initials: A
authors.lastname: Bankevich
authors.affiliation: Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia, Department of Mathematics and Mechanics, Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia and Department of Computer Science and Engineering, University of California, San Diego, USA.
authors.forename: Alexey
authors.initials: A
authors.lastname: Gurevich
authors.affiliation: Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia, Department of Mathematics and Mechanics, Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia and Department of Computer Science and Engineering, University of California, San Diego, USA.
authors.forename: Tatiana
authors.initials: T
authors.lastname: Krivosheeva
authors.affiliation: Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia, Department of Mathematics and Mechanics, Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia and Department of Computer Science and Engineering, University of California, San Diego, USA.
authors.forename: Sergey
authors.initials: S
authors.lastname: Nurk
authors.affiliation: Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia, Department of Mathematics and Mechanics, Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia and Department of Computer Science and Engineering, University of California, San Diego, USA.
authors.forename: Son
authors.initials: S
authors.lastname: Pham
authors.affiliation: Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia, Department of Mathematics and Mechanics, Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia and Department of Computer Science and Engineering, University of California, San Diego, USAAlgorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia, Department of Mathematics and Mechanics, Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia and Department of Computer Science and Engineering, University of California, San Diego, USA.
authors.forename: Anton
authors.initials: A
authors.lastname: Korobeynikov
authors.affiliation: Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia, Department of Mathematics and Mechanics, Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia and Department of Computer Science and Engineering, University of California, San Diego, USAAlgorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia, Department of Mathematics and Mechanics, Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia and Department of Computer Science and Engineering, University of California, San Diego, USA.
authors.forename: Alla
authors.initials: A
authors.lastname: Lapidus
authors.affiliation: Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia, Department of Mathematics and Mechanics, Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia and Department of Computer Science and Engineering, University of California, San Diego, USAAlgorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia, Department of Mathematics and Mechanics, Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia and Department of Computer Science and Engineering, University of California, San Diego, USA.
authors.forename: Pavel A
authors.initials: PA
authors.lastname: Pevzner
mesh_terms: D000192:Actinomycetales / Q000235:genetics; D000465:Algorithms; D004247:DNA / Q000737:chemistry; D015723:Gene Library; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA / Q000379:methods*; D013211:Staphylococcus aureus / Q000235:genetics
chemical_list: D004247:DNA