Transposon insertion sequencing data analysis bioinformatics software tools
We use the term Tn-seq to refer to a range of transposon insertion sequencing techniques that use a random transposon mutant library and high-throughput sequencing to study fitness of mutant strains and/or to identify genes that are essential or advantageous for growth under a…
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TnSeq
Desktop

TnSeq

A zero-inflated Poisson model for analyzing the Tn-seq data that are…

A zero-inflated Poisson model for analyzing the Tn-seq data that are high-dimensional and with an excess of zeros. Maximum likelihood estimates of model parameters are obtained using an…

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Bio-Tradis
Desktop

Bio-Tradis

Contains a set of tools to analyse the output from TraDIS analyses. Bio-Tradis…

Contains a set of tools to analyse the output from TraDIS analyses. Bio-Tradis provides functionality to (i) detect TraDIS tags in a BAM file, (ii) add the tags to the reads, (iii) filter reads in a…

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GeIST
Desktop

GeIST Genomic Integration Site Tracker

A command-line pipeline designed to map integration sites. GeIST bridges the…

A command-line pipeline designed to map integration sites. GeIST bridges the gap between raw sequence data and identifying genomic DNA integration sites in multiple samples or parsing independent…

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TRANSIT
Desktop

TRANSIT

A tool for analyzing Himar1 TnSeq data. TRANSIT provides a graphical interface…

A tool for analyzing Himar1 TnSeq data. TRANSIT provides a graphical interface to three different statistical methods for analyzing TnSeq data. These methods cover a variety of approaches capable of…

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ARTIST
Desktop

ARTIST

An accessible transposon-insertion sequencing (TIS) analysis pipeline for…

An accessible transposon-insertion sequencing (TIS) analysis pipeline for identifying essential regions that are required for growth under optimal conditions as well as conditionally essential loci…

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Tn-seq explorer
Desktop

Tn-seq explorer

A convenient and easy-to-use package of tools for exploration of the Tn-seq…

A convenient and easy-to-use package of tools for exploration of the Tn-seq data. In a typical application, the user will have obtained a collection of sequence reads adjacent to transposon…

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ESSENTIALS
Desktop
Web

ESSENTIALS

A software tool for researchers in the genomics field utilizing transposon…

A software tool for researchers in the genomics field utilizing transposon insertion sequencing analysis. ESSENTIALS accurately predicts (conditionally) essential genes and offers the flexibility of…

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Tn-HMM
Desktop

Tn-HMM

A method for analyzing sequence data from transposon mutant libraries using a…

A method for analyzing sequence data from transposon mutant libraries using a Hidden Markov Model (HMM), along with formulas to adapt the parameters of the model to different datasets for robustness.…

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Tn-seq
Desktop

Tn-seq

Custom scripts for analyzing (parsing, mapping, and tallying) Tn-seq reads and…

Custom scripts for analyzing (parsing, mapping, and tallying) Tn-seq reads and determining differentially abundant transposon insertion mutants. The scripts contained herein can be used to…

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