title: Telescoper: de novo assembly of highly repetitive regions.
abstract: BACKGROUND
  With advances in sequencing technology, it has become faster and cheaper to obtain short-read data from which to assemble genomes. Although there has been considerable progress in the field of genome assembly, producing high-quality de novo assemblies from short-reads remains challenging, primarily because of the complex repeat structures found in the genomes of most higher organisms. The telomeric regions of many genomes are particularly difficult to assemble, though much could be gained from the study of these regions, as their evolution has not been fully characterized and they have been linked to aging.
  
  
  RESULTS
  In this article, we tackle the problem of assembling highly repetitive regions by developing a novel algorithm that iteratively extends long paths through a series of read-overlap graphs and evaluates them based on a statistical framework. Our algorithm, Telescoper, uses short- and long-insert libraries in an integrated way throughout the assembly process. Results on real and simulated data demonstrate that our approach can effectively resolve much of the complex repeat structures found in the telomeres of yeast genomes, especially when longer long-insert libraries are used.
  
  
  BACKGROUND
  Telescoper is publicly available for download at sourceforge.net/p/telescoper.
  
  
  BACKGROUND
  yss@eecs.berkeley.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of EECS, University of California, Berkeley, CA 94720, USA.
authors.forename: Ma'ayan
authors.initials: M
authors.lastname: Bresler
authors.forename: Sara
authors.initials: S
authors.lastname: Sheehan
authors.forename: Andrew H
authors.initials: AH
authors.lastname: Chan
authors.forename: Yun S
authors.initials: YS
authors.lastname: Song
mesh_terms: D000465:Algorithms; D004247:DNA / Q000737:chemistry; D016678:Genome; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D012091:Repetitive Sequences, Nucleic Acid; D012441:Saccharomyces cerevisiae / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004247:DNA