Abstract
Tn-seq is a high throughput technique for analysis of transposon mutant libraries. Tn-seq Explorer was developed as 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 insertions in a reference genome. The reads are first aligned to the reference genome using one of the tools available for this task. Tn-seq Explorer reads the alignment and the gene annotation, and provides the user with a set of tools to investigate the data and identify possibly essential or advantageous genes as those that contain significantly low counts of transposon insertions. Emphasis is placed on providing flexibility in selecting parameters and methodology most appropriate for each particular dataset. Tn-seq Explorer is written in Java as a menu-driven, stand-alone application. It was tested on Windows, Mac OS, and Linux operating systems. The source code is distributed under the terms of GNU General Public License. The program and the source code are available for download at http://www.cmbl.uga.edu/downloads/programs/Tn_seq_Explorer/ and https://github.com/sina-cb/Tn-seqExplorer.
Highlights
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 specific set of conditions
The primary input is the alignment of sequence reads to the reference genome in the SAM format [17]
Popular tools for alignment of sequence reads to a reference genome sequence, such as Burrows-Wheeler Aligner (BWA) [18] or Bowtie [19], can generate the SAM-formatted output
Summary
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 specific set of conditions. Thanks to the novel advances in deep sequencing technologies, this technique has become useful for understanding gene function and the genetics behind microbial physiology. Even though the rationale and the overall technique of Tn-seq is straightforward, there are different variations in the methodology to achieve the expected results [4]. Tn-Seq Explorer any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section
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