The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries

Bioinformatics
Lars BarquistJulian Parkhill

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.

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Citations

Sep 28, 2016·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Lars BarquistJörg Vogel
Feb 16, 2017·Scientific Reports·Bimal JanaLuca Guardabassi
Nov 10, 2018·Environmental Microbiology·Anne LorenzSusanne Häussler
Dec 5, 2018·Journal of Bacteriology·Connor SharpColin Kleanthous
Feb 6, 2019·Microbial Genomics·Christine J BoinettStephen Baker
Jun 5, 2020·JCI Insight·Luchang ZhuJames M Musser
Jul 18, 2020·PLoS Computational Biology·Andrew J PageIan G Charles
Jun 10, 2020·Infection and Immunity·Francesca L ShortPeter W Taylor
Jul 18, 2017·PLoS Computational Biology·Nick FysonCaroline Colijn
Jul 19, 2017·Scientific Reports·Lorena RuizDouwe van Sinderen
Sep 16, 2018·Applied and Environmental Microbiology·Jacob H CecilJoshua K Michener
Jan 23, 2019·The Journal of Clinical Investigation·Harry R Hill
Apr 8, 2020·Frontiers in Plant Science·Belinda K FabianIan T Paulsen
Jan 23, 2019·The Journal of Clinical Investigation·Luchang ZhuJames M Musser
Apr 20, 2019·Frontiers in Microbiology·Iva Atanaskovic, Colin Kleanthous
Jun 25, 2020·Nature Communications·Alysha G ElliottMatthew A Cooper
Mar 24, 2017·Nucleic Acids Research·Michael A DeJesusThomas R Ioerger
Jun 10, 2020·The Journal of Antimicrobial Chemotherapy·A Keith TurnerJohn Wain
Jun 2, 2017·BMC Genomics·Amelia R L CharbonneauAndrew S Waller
Jun 14, 2020·Nature Reviews. Genetics·Amy K CainTim van Opijnen
Oct 20, 2020·Microbial Genomics·Hannah G HamptonPeter C Fineran
Sep 5, 2020·Annual Review of Genetics·Tim van Opijnen, Henry L Levin
Jan 9, 2021·Frontiers in Genetics·Ellen M E SykesAyush Kumar

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