title: TwoPaCo: an efficient algorithm to build the compacted de Bruijn graph from many complete genomes.
abstract: BACKGROUND
  de Bruijn graphs have been proposed as a data structure to facilitate the analysis of related whole genome sequences, in both a population and comparative genomic settings. However, current approaches do not scale well to many genomes of large size (such as mammalian genomes).
  
  
  RESULTS
  In this article, we present TwoPaCo, a simple and scalable low memory algorithm for the direct construction of the compacted de Bruijn graph from a set of complete genomes. We demonstrate that it can construct the graph for 100 simulated human genomes in less than a day and eight real primates in < 2 h, on a typical shared-memory machine. We believe that this progress will enable novel biological analyses of hundreds of mammalian-sized genomes.
  
  
  METHODS
  Our code and data is available for download from github.com/medvedevgroup/TwoPaCo.
  
  
  BACKGROUND
  ium125@psu.edu.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA.
authors.forename: Ilia
authors.initials: I
authors.lastname: Minkin
authors.affiliation: BioTuring Inc., San Diego, CA 92121, USA.
authors.forename: Son
authors.initials: S
authors.lastname: Pham
authors.affiliation: Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA.|Department of Biochemistry and Molecular Biology.|Genomic Sciences Institute of the Huck, The Pennsylvania State University, University Park, PA 16802, USA.
authors.forename: Paul
authors.initials: P
authors.lastname: Medvedev
mesh_terms: D000465:Algorithms; D000818:Animals; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D006801:Humans; D011323:Primates / Q000235:genetics; D012984:Software