ESSENTIALS: Software for Rapid Analysis of High Throughput Transposon Insertion Sequencing Data
Open Access
- 10 August 2012
- journal article
- research article
- Published by Public Library of Science (PLoS) in PLOS ONE
- Vol. 7 (8), e43012
- https://doi.org/10.1371/journal.pone.0043012
Abstract
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.Keywords
This publication has 25 references indexed in Scilit:
- OGEE: an online gene essentiality databaseNucleic Acids Research, 2011
- High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosomeGenome Research, 2011
- The essential genome of a bacteriumMolecular Systems Biology, 2011
- The European Nucleotide ArchiveNucleic Acids Research, 2010
- edgeR: a Bioconductor package for differential expression analysis of digital gene expression dataBioinformatics, 2009
- Tracking insertion mutants within libraries by deep sequencing and a genome-wide screen for Haemophilus genes required in the lungProceedings of the National Academy of Sciences of the United States of America, 2009
- Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganismsNature Methods, 2009
- Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its HabitatCell Host & Microbe, 2009
- Targeting a bacterial stress response to enhance antibiotic actionProceedings of the National Academy of Sciences of the United States of America, 2009
- Construction of consecutive deletions of the Escherichia coli chromosomeMolecular Systems Biology, 2007