title: The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries.
abstract: Transposon insertion sequencing is a high-throughput technique for assaying large libraries of otherwise isogenic transposon mutants providing insight into gene essentiality, gene function and genetic interactions. We previously developed the Transposon Directed Insertion Sequencing (TraDIS) protocol for this purpose, which utilizes shearing of genomic DNA followed by specific PCR amplification of transposon-containing fragments and Illumina sequencing. Here we describe an optimized high-yield library preparation and sequencing protocol for TraDIS experiments and a novel software pipeline for analysis of the resulting data. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools. This article can serve as a general reference for the application of the TraDIS methodology.
  
  
  
  The optimized sequencing protocol is included as supplementary information. The Bio-Tradis analysis pipeline is available under a GPL license at https://github.com/sanger-pathogens/Bio-Tradis
  
  
  
  parkhill@sanger.ac.uk
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and Institute for Molecular Infection Biology, University of Würzburg, Würzburg D-97080, Germany.
authors.forename: Lars
authors.initials: L
authors.lastname: Barquist
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and.
authors.forename: Matthew
authors.initials: M
authors.lastname: Mayho
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and.
authors.forename: Carla
authors.initials: C
authors.lastname: Cummins
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and.
authors.forename: Amy K
authors.initials: AK
authors.lastname: Cain
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and.
authors.forename: Christine J
authors.initials: CJ
authors.lastname: Boinett
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Page
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and.
authors.forename: Gemma C
authors.initials: GC
authors.lastname: Langridge
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Quail
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and.
authors.forename: Jacqueline A
authors.initials: JA
authors.lastname: Keane
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and.
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
mesh_terms: D004251:DNA Transposable Elements; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing; D012984:Software
chemical_list: D004251:DNA Transposable Elements