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

Summary: 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...

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Main Authors:	Barquist, Lars, Mayho, Matthew, Cummins, Carla, Cain, Amy K., Boinett, Christine J., Page, Andrew J., Langridge, Gemma C., Quail, Michael A., Keane, Jacqueline A., Parkhill, Julian
Format:	Online
Language:	English
Published:	Oxford University Press 2016
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4896371/

id	pubmed-4896371
recordtype	oai_dc
spelling	pubmed-48963712016-06-09 The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries Barquist, Lars Mayho, Matthew Cummins, Carla Cain, Amy K. Boinett, Christine J. Page, Andrew J. Langridge, Gemma C. Quail, Michael A. Keane, Jacqueline A. Parkhill, Julian Applications Notes Summary: 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. Oxford University Press 2016-04-01 2016-01-21 /pmc/articles/PMC4896371/ /pubmed/26794317 http://dx.doi.org/10.1093/bioinformatics/btw022 Text en © The Author 2015. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Barquist, Lars Mayho, Matthew Cummins, Carla Cain, Amy K. Boinett, Christine J. Page, Andrew J. Langridge, Gemma C. Quail, Michael A. Keane, Jacqueline A. Parkhill, Julian
spellingShingle	Barquist, Lars Mayho, Matthew Cummins, Carla Cain, Amy K. Boinett, Christine J. Page, Andrew J. Langridge, Gemma C. Quail, Michael A. Keane, Jacqueline A. Parkhill, Julian The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries
author_facet	Barquist, Lars Mayho, Matthew Cummins, Carla Cain, Amy K. Boinett, Christine J. Page, Andrew J. Langridge, Gemma C. Quail, Michael A. Keane, Jacqueline A. Parkhill, Julian
author_sort	Barquist, Lars
title	The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries
title_short	The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries
title_full	The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries
title_fullStr	The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries
title_full_unstemmed	The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries
title_sort	tradis toolkit: sequencing and analysis for dense transposon mutant libraries
description	Summary: 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.
publisher	Oxford University Press
publishDate	2016
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4896371/
_version_	1613590270451908608

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

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