ESSENTIALS: software for rapid analysis of high throughput transposon insertion sequencing data.

High-throughput analysis of genome-wide random transposon mutant libraries is a powerful tool for (conditional) essential gene discovery. Recently, several next-generation sequencing approaches, e.g. Tn-seq/INseq, HITS and TraDIS, have been developed that accurately map the site of transposon insert...

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Autores principales:	Aldert Zomer, Peter Burghout, Hester J Bootsma, Peter W M Hermans, Sacha A F T van Hijum
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/805561fa1c3846d6a54e7c175dc04764
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spelling	oai:doaj.org-article:805561fa1c3846d6a54e7c175dc047642021-11-18T07:09:03ZESSENTIALS: software for rapid analysis of high throughput transposon insertion sequencing data.1932-620310.1371/journal.pone.0043012https://doaj.org/article/805561fa1c3846d6a54e7c175dc047642012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22900082/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203High-throughput analysis of genome-wide random transposon mutant libraries is a powerful tool for (conditional) essential gene discovery. Recently, several next-generation sequencing approaches, e.g. Tn-seq/INseq, HITS and TraDIS, have been developed that accurately map the site of transposon insertions by mutant-specific amplification and sequence readout of DNA flanking the transposon insertions site, assigning a measure of essentiality based on the number of reads per insertion site flanking sequence or per gene. However, analysis of these large and complex datasets is hampered by the lack of an easy to use and automated tool for transposon insertion sequencing data. To fill this gap, we developed ESSENTIALS, an open source, web-based software tool for researchers in the genomics field utilizing transposon insertion sequencing analysis. It accurately predicts (conditionally) essential genes and offers the flexibility of using different sample normalization methods, genomic location bias correction, data preprocessing steps, appropriate statistical tests and various visualizations to examine the results, while requiring only a minimum of input and hands-on work from the researcher. We successfully applied ESSENTIALS to in-house and published Tn-seq, TraDIS and HITS datasets and we show that the various pre- and post-processing steps on the sequence reads and count data with ESSENTIALS considerably improve the sensitivity and specificity of predicted gene essentiality.Aldert ZomerPeter BurghoutHester J BootsmaPeter W M HermansSacha A F T van HijumPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 8, p e43012 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Aldert Zomer Peter Burghout Hester J Bootsma Peter W M Hermans Sacha A F T van Hijum ESSENTIALS: software for rapid analysis of high throughput transposon insertion sequencing data.
description	High-throughput analysis of genome-wide random transposon mutant libraries is a powerful tool for (conditional) essential gene discovery. Recently, several next-generation sequencing approaches, e.g. Tn-seq/INseq, HITS and TraDIS, have been developed that accurately map the site of transposon insertions by mutant-specific amplification and sequence readout of DNA flanking the transposon insertions site, assigning a measure of essentiality based on the number of reads per insertion site flanking sequence or per gene. However, analysis of these large and complex datasets is hampered by the lack of an easy to use and automated tool for transposon insertion sequencing data. To fill this gap, we developed ESSENTIALS, an open source, web-based software tool for researchers in the genomics field utilizing transposon insertion sequencing analysis. It accurately predicts (conditionally) essential genes and offers the flexibility of using different sample normalization methods, genomic location bias correction, data preprocessing steps, appropriate statistical tests and various visualizations to examine the results, while requiring only a minimum of input and hands-on work from the researcher. We successfully applied ESSENTIALS to in-house and published Tn-seq, TraDIS and HITS datasets and we show that the various pre- and post-processing steps on the sequence reads and count data with ESSENTIALS considerably improve the sensitivity and specificity of predicted gene essentiality.
format	article
author	Aldert Zomer Peter Burghout Hester J Bootsma Peter W M Hermans Sacha A F T van Hijum
author_facet	Aldert Zomer Peter Burghout Hester J Bootsma Peter W M Hermans Sacha A F T van Hijum
author_sort	Aldert Zomer
title	ESSENTIALS: software for rapid analysis of high throughput transposon insertion sequencing data.
title_short	ESSENTIALS: software for rapid analysis of high throughput transposon insertion sequencing data.
title_full	ESSENTIALS: software for rapid analysis of high throughput transposon insertion sequencing data.
title_fullStr	ESSENTIALS: software for rapid analysis of high throughput transposon insertion sequencing data.
title_full_unstemmed	ESSENTIALS: software for rapid analysis of high throughput transposon insertion sequencing data.
title_sort	essentials: software for rapid analysis of high throughput transposon insertion sequencing data.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/805561fa1c3846d6a54e7c175dc04764
work_keys_str_mv	AT aldertzomer essentialssoftwareforrapidanalysisofhighthroughputtransposoninsertionsequencingdata AT peterburghout essentialssoftwareforrapidanalysisofhighthroughputtransposoninsertionsequencingdata AT hesterjbootsma essentialssoftwareforrapidanalysisofhighthroughputtransposoninsertionsequencingdata AT peterwmhermans essentialssoftwareforrapidanalysisofhighthroughputtransposoninsertionsequencingdata AT sachaaftvanhijum essentialssoftwareforrapidanalysisofhighthroughputtransposoninsertionsequencingdata
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ESSENTIALS: software for rapid analysis of high throughput transposon insertion sequencing data.

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