Tn-seq explorer: a tool for analysis of high-throughput sequencing data of transposon mutant libraries

• Published in: PloS one Vol. 10; no. 5; p. e0126070
• Main Authors: Solaimanpour, Sina, Sarmiento, Felipe, Mrázek, Jan
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 04-05-2015; Public Library of Science (PLoS)
• Subjects: Analysis; Annotations; Bacteria - genetics; Bioinformatics; Cell cycle; Computational Biology - methods; Data analysis; Data processing; Databases, Nucleic Acid; Deoxyribonucleic acid; DNA; DNA Transposable Elements; Downloading; Gene Library; Gene mutation; Genes; Genomes; Genomics - methods; High-Throughput Nucleotide Sequencing; High-throughput screening (Biochemical assaying); Influence; Java (programming language); Methods; Microorganisms; Mutation; Next-generation sequencing; Nucleotide sequence; Operating systems; Software; Source code; Target recognition; Transposons
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0126070

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.