ArticleBioinformatics (Oxford, England)2016
The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 167 papers.
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Who cites it
167 citing papers in PubMed.
- Construction of Inducible Transposon Mutant Libraries in Chlamydia trachomatis.Methods in molecular biology (Clifton, N.J.) · 2027Article
- High-throughput transposon sequencing identifies HprR as a key regulator of the LEE operon and virulence inVirulence · 2026Article
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- Genome-wide identification of conditionally essential genes for growth in the presence of sulfamethoxazole and trimethoprim in sulfamethoxazole- and trimethoprim-resistantMicrobiology spectrum · 2026Article
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- L-type pyocins inhibit the BAM complex to kill without cell entry.Nature communications · 2026Article
- Mapping the genomic landscape of antibiotic susceptiblity in Escherichia coli.npj antimicrobials and resistance · 2026Article
- Profiling of genetic determinants required for fitness of community-associated methicillin-resistantMicrobiology spectrum · 2026Article
- Comparative analysis of gene importance inmSystems · 2026Article
- Unravelling the unique essential genes ofMicrobial genomics · 2026Article
- Mutations that confer resistance to sodium azide affect the levels of two physiological isoforms of SecA inMicrobiology (Reading, England) · 2026Article
- Discovery of HAdvanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Genome-wide analysis exploring mechanisms used bymSystems · 2026Article
- NetCIS: a network-based common insertion site pipeline for case-control Sleeping Beauty screens.Briefings in bioinformatics · 2026Article
- ConNIS and labeling instability: New statistical methods for improving the detection of essential genes in TraDIS libraries.PLoS computational biology · 2026Article
- Article
- Article
- Phage receptor specificity drives cross-resistance patterns and governs fitness trade-offs during sequential resistance acquisition in Salmonella.The ISME journal · 2026Article
- What makes them stick? A genetic analysis of biofilm formation of an infective endocarditis-causingFrontiers in cellular and infection microbiology · 2026Article
107 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors.
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Abstract
unlabelledTransposon 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. AVAILABILITY AND IMPLEMENTATION: 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 CONTACT: parkhill@sanger.ac.uk SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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