Lasse Maretty Sørensen

Sensitive detection of circular DNAs at single-nucleotide resolution using guided realignment of partially aligned reads

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  • Iñigo Prada-Luengo, University of Copenhagen
  • ,
  • Anders Krogh, University of Copenhagen
  • ,
  • Lasse Maretty
  • Birgitte Regenberg, University of Copenhagen

BACKGROUND: Circular DNA has recently been identified across different species including human normal and cancerous tissue, but short-read mappers are unable to align many of the reads crossing circle junctions hence limiting their detection from short-read sequencing data. RESULTS: Here, we propose a new method, Circle-Map that guides the realignment of partially aligned reads using information from discordantly mapped reads to map the short unaligned portions using a probabilistic model. We compared Circle-Map to similar up-to-date methods for circular DNA and RNA detection and we demonstrate how the approach implemented in Circle-Map dramatically increases sensitivity for detection of circular DNA on both simulated and real data while retaining high precision. CONCLUSION: Circle-Map is an easy-to-use command line tool that implements the required pipeline to accurately detect circular DNA from circle enriched next generation sequencing experiments. Circle-Map is implemented in python3.6 and it is freely available at

Original languageEnglish
Article number663
JournalBMC Bioinformatics
Number of pages9
Publication statusPublished - Dec 2019

    Research areas

  • circRNA, eccDNA, ecDNA, Extra chromosomal circular DNA, Next generation sequencing, Structural variation

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