title: Jitterbug: somatic and germline transposon insertion detection at single-nucleotide resolution.
abstract: BACKGROUND
  Transposable elements are major players in genome evolution. Transposon insertion polymorphisms can translate into phenotypic differences in plants and animals and are linked to different diseases including human cancer, making their characterization highly relevant to the study of genome evolution and genetic diseases.
  
  
  RESULTS
  Here we present Jitterbug, a novel tool that identifies transposable element insertion sites at single-nucleotide resolution based on the pairedend mapping and clipped-read signatures produced by NGS alignments. Jitterbug can be easily integrated into existing NGS analysis pipelines, using the standard BAM format produced by frequently applied alignment tools (e.g. bwa, bowtie2), with no need to realign reads to a set of consensus transposon sequences. Jitterbug is highly sensitive and able to recall transposon insertions with a very high specificity, as demonstrated by benchmarks in the human and Arabidopsis genomes, and validation using long PacBio reads. In addition, Jitterbug estimates the zygosity of transposon insertions with high accuracy and can also identify somatic insertions.
  
  
  CONCLUSIONS
  We demonstrate that Jitterbug can identify mosaic somatic transposon movement using sequenced tumor-normal sample pairs and allows for estimating the cancer cell fraction of clones containing a somatic TE insertion. We suggest that the independent methods we use to evaluate performance are a step towards creating a gold standard dataset for benchmarking structural variant prediction tools.
authors.affiliation: Genomic and Epigenomic Variation in Disease Group, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain. elizabeth.m.henaff@gmail.com.|Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Barcelona, Spain. elizabeth.m.henaff@gmail.com.|current address: Weill Cornell Medical College, Institute for Computational Biomedicine, 1305 York Avenue, New York, NY, 10021, USA. elizabeth.m.henaff@gmail.com.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Hénaff
authors.affiliation: Genomic and Epigenomic Variation in Disease Group, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain. luis.zapata@crg.eu.|Universitat Pompeu Fabra (UPF), Barcelona, Spain. luis.zapata@crg.eu.
authors.forename: Luís
authors.initials: L
authors.lastname: Zapata
authors.affiliation: Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Barcelona, Spain. josep.casacuberta@cragenomica.es.
authors.forename: Josep M
authors.initials: JM
authors.lastname: Casacuberta
authors.affiliation: Genomic and Epigenomic Variation in Disease Group, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain. Stephan.Ossowski@crg.eu.|Universitat Pompeu Fabra (UPF), Barcelona, Spain. Stephan.Ossowski@crg.eu.
authors.forename: Stephan
authors.initials: S
authors.lastname: Ossowski
mesh_terms: D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D004251:DNA Transposable Elements; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D005854:Germ Cells / Q000378:metabolism*; D006720:Homozygote; D006801:Humans; D016254:Mutagenesis, Insertional; D009369:Neoplasms / Q000235:genetics; D011110:Polymorphism, Genetic; D015203:Reproducibility of Results; D012984:Software
chemical_list: D004251:DNA Transposable Elements