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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…
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TnSeq
Desktop

TnSeq

Identifies conditionally essential genes. TnSeq is a zero-inflated Poisson…

Identifies conditionally essential genes. TnSeq is a zero-inflated Poisson (ZIP) model to deal with the excess of zeros for the analysis of transposon insertion sequencing (Tn-seq) data at the level…

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MAGenTA
Desktop

MAGenTA Microbial Assessment by Genome-wide Tn-Seq Analysis

Represents a suite of analysis tools concerning the calculation of the…

Represents a suite of analysis tools concerning the calculation of the development rate for disrupted gene in the genome. MAGenTA is a complete Tn-Seq analysis pipeline implemented in Galaxy, but…

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INSPIIRED
Desktop

INSPIIRED INtegration Site PIpeline for pairedend REaDs

Allows to work about viral integration sites and the longitudinal outcomes of…

Allows to work about viral integration sites and the longitudinal outcomes of gene therapy patients. INSPIIRED serves for quantitative analysis of integration site distributions. This is a…

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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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