title: FinisherSC: a repeat-aware tool for upgrading de novo assembly using long reads.
abstract: We introduce FinisherSC, a repeat-aware and scalable tool for upgrading de novo assembly using long reads. Experiments with real data suggest that FinisherSC can provide longer and higher quality contigs than existing tools while maintaining high concordance.
  
  
  METHODS
  The tool and data are available and will be maintained at http://kakitone.github.io/finishingTool/
  
  
  BACKGROUND
  : dntse@stanford.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Electrical Engineering and Computer Sciences, UC Berkeley.
authors.forename: Ka-Kit
authors.initials: KK
authors.lastname: Lam
authors.affiliation: U.S. Department of Energy Joint Genome Institute, Walnut Creek.
authors.forename: Kurt
authors.initials: K
authors.lastname: LaButti
authors.affiliation: Pacific Biosciences, Menlo Park, and.
authors.forename: Asif
authors.initials: A
authors.lastname: Khalak
authors.affiliation: Department of Electrical Engineering and Computer Sciences, UC Berkeley, Department of Electrical Engineering, Stanford University, Palo Alto, CA, USA.
authors.forename: David
authors.initials: D
authors.lastname: Tse
mesh_terms: D000465:Algorithms; D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D004330:Drosophila / Q000235:genetics; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D015233:Models, Statistical; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software