8b54dda796c42550ec109101d6317c56 mobdna_a2019m12v10p53.pdf f81ef5bc500da3efbc4ce9d4c0dcf6d180756a64 mobdna_a2019m12v10p53.pdf c64d52c12403e3ca04e19911471f2eec2c03a18daa206d11c32dda287c79f37a mobdna_a2019m12v10p53.pdf Title: A benchmark of transposon insertion detection tools using real data Subject: Mobile DNA, 2019, doi:10.1186/s13100-019-0197-9 Keywords: Benchmark,Transposable elements,Polymorphism,Transposon insertion,Resequencing Author: Pol Vendrell-Mir Creator: Arbortext Advanced Print Publisher 9.1.440/W Unicode Producer: Acrobat Distiller 10.0.0 (Windows); modified using iText® 5.3.5 ©2000-2012 1T3XT BVBA (SPRINGER SBM; licensed version) CreationDate: Sun Dec 29 11:03:03 2019 CET ModDate: Mon Dec 30 13:56:16 2019 CET Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 19 Encrypted: no Page size: 595.276 x 790.866 pts Page rot: 0 File size: 3676287 bytes Optimized: no PDF version: 1.3 name type encoding emb sub uni object ID 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SinglePage PageMode: UseNone Outlines: Item: Title: Abstract Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@61baa894 Children: Item: Title: Background Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@b065c63 Item: Title: Results Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@768debd Item: Title: Conclusions Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@490d6c15 Item: Title: Background Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@7d4793a8 Item: Title: Results Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@449b2d27 Children: Item: Title: Tools selected for benchmarking Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@5479e3f Item: Title: LTR-retrotransposon and MITE landscape in Nipponbare and MH63 genomes Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@27082746 Item: Title: Annotation of standard transposon insertion datasets for tool benchmarking Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@66133adc Item: Title: Detection of reference insertions by broad-spectrum tools Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@7bfcd12c Item: Title: Detection of non-reference insertions by broad-spectrum tools Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@42f30e0a Item: Title: Detection of non-reference insertions by family-specific tools Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@24273305 Item: Title: Overlap between TIP prediction tools Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@5b1d2887 Item: Title: Combining tools to improve sensitivity Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@46f5f779 Item: Title: Evaluation of best-performing tools using Drosophila and human datasets Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1c2c22f3 Item: Title: Running time Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@18e8568 Item: Title: Discussion Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@33e5ccce Children: Item: Title: The use of real data is essential for an accurate benchmarking of TE insertion detection tools Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@5a42bbf4 Item: Title: Tool performance varies depending on TE family Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@270421f5 Item: Title: Influence of the type of genome on the performance of the tools Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@52d455b8 Item: Title: Sequencing coverage critically impacts TIP detection Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@4f4a7090 Item: Title: Strategies to increase tool performance Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@18ef96 Item: Title: Selecting the appropriate tools for detecting TE insertions in resequencing data Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@6956de9 Item: Title: Conclusions Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@769c9116 Item: Title: Methods Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@6aceb1a5 Children: Item: Title: Sequence data used Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@2d6d8735 Item: Title: MITE annotation Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@ba4d54 Item: Title: LTR-retrotransposon annotation Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@12bc6874 Item: Title: Determination of benchmarking standards Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@de0a01f Item: Title: Drosophila and human benchmarking datasets Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@4c75cab9 Item: Title: TIP prediction Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1ef7fe8e Item: Title: Evaluation parameters Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@6f79caec Item: Title: Supplementary information Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@67117f44 Item: Title: Acknowledgements Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@5d3411d Item: Title: Authors’ contributions Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@2471cca7 Item: Title: Funding Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@5fe5c6f Item: Title: Availability of data and materials Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@6979e8cb Item: Title: Ethics approval and consent to participate Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@763d9750 Item: Title: Consent for publication Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@5c0369c4 Item: Title: Competing interests Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@2be94b0f Item: Title: 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