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Bioinformatics. 2016 Apr 1;32(7):1109-11. doi: 10.1093/bioinformatics/btw022. Epub 2016 Jan 21.

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

Author information

1
Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and Institute for Molecular Infection Biology, University of Würzburg, Würzburg D-97080, Germany.
2
Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and.

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.

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.

PMID:
26794317
PMCID:
PMC4896371
DOI:
10.1093/bioinformatics/btw022
[Indexed for MEDLINE]
Free PMC Article

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