Facilitated sequence assembly using densely labeled optical DNA barcodes: A combinatorial auction approach

Research output: Contribution to journalArticle


The output from whole genome sequencing is a set of contigs, i.e. short non-overlapping DNA sequences (sizes 1-100 kilobasepairs). Piecing the contigs together is an especially difficult task for previously unsequenced DNA, and may not be feasible due to factors such as the lack of sufficient coverage or larger repetitive regions which generate gaps in the final sequence. Here we propose a new method for scaffolding such contigs. The proposed method uses densely labeled optical DNA barcodes from competitive binding experiments as scaffolds. On these scaffolds we position theoretical barcodes which are calculated from the contig sequences. This allows us to construct longer DNA sequences from the contig sequences. This proof-of-principle study extends previous studies which use sparsely labeled DNA barcodes for scaffolding purposes. Our method applies a probabilistic approach that allows us to discard “foreign” contigs from mixed samples with contigs from different types of DNA. We satisfy the contig non-overlap constraint by formulating the contig placement challenge as a combinatorial auction problem. Our exact algorithm for solving this problem reduces computational costs compared to previous methods in the combinatorial auction field. We demonstrate the usefulness of the proposed scaffolding method both for synthetic contigs and for contigs obtained using Illumina sequencing for a mixed sample with plasmid and chromosomal DNA.


  • Albertas Dvirnas
  • Christoffer Pichler
  • Callum L. Stewart
  • Saair Quaderi
  • Lena K. Nyberg
  • Vilhelm Müller
  • Santosh Kumar Bikkarolla
  • Erik Kristiansson
  • Linus Sandegren
  • Fredrik Westerlund
  • Tobias Ambjörnsson
External organisations
  • Chalmers University of Technology
  • Uppsala University
  • Lund University
Research areas and keywords

Subject classification (UKÄ) – MANDATORY

  • Genetics
  • Biophysics
Original languageEnglish
Article numbere0193900
JournalPLoS ONE
Issue number3
Publication statusPublished - 2018 Mar 1
Publication categoryResearch