MAGenTA: a Galaxy implemented tool for complete Tn-Seq analysis and data visualization

Bioinformatics
Katherine Maia McCoyTim van Opijnen

Abstract

Transposon insertion sequencing (Tn-Seq) is a microbial systems-level tool, that can determine on a genome-wide scale and in high-throughput, whether a gene, or a specific genomic region, is important for fitness under a specific experimental condition. Here, we present MAGenTA, a suite of analysis tools which accurately calculate the growth rate for each disrupted gene in the genome to enable the discovery of: (i) new leads for gene function, (ii) non-coding RNAs; (iii) genes, pathways and ncRNAs that are involved in tolerating drugs or induce disease; (iv) higher order genome organization; and (v) host-factors that affect bacterial host susceptibility. MAGenTA is a complete Tn-Seq analysis pipeline making sensitive genome-wide fitness (i.e. growth rate) analysis available for most transposons and Tn-Seq associated approaches (e.g. TraDis, HiTS, IN-Seq) and includes fitness (growth rate) calculations, sliding window analysis, bottleneck calculations and corrections, statistics to compare experiments and strains and genome-wide fitness visualization. MAGenTA is available at the Galaxy public ToolShed repository and all source code can be found and are freely available at https://vanopijnenlab.github.io/MAGenTA/ . vanopijn@bc.ed...Continue Reading

References

Sep 15, 2009·Cell Host & Microbe·Andrew L GoodmanJeffrey I Gordon
Oct 7, 2009·Proceedings of the National Academy of Sciences of the United States of America·Jeffrey D GawronskiBrian J Akerley
Oct 15, 2009·Genome Research·Gemma C LangridgeA Keith Turner
Jul 19, 2012·PLoS Pathogens·Beth MannJason W Rosch
Jul 25, 2012·Genome Research·Tim van Opijnen, Andrew Camilli
May 29, 2013·Nature Reviews. Microbiology·Tim van Opijnen, Andrew Camilli
May 23, 2015·Scientific Reports·Yoann Le BretonKevin S McIver

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Citations

Feb 11, 2019·Molecular Oral Microbiology·Robert C Shields, Paul A Jensen
Jun 14, 2020·Nature Reviews. Genetics·Amy K CainTim van Opijnen
Jan 19, 2020·BMC Bioinformatics·Defne Surujon, Tim van Opijnen
Sep 5, 2020·Annual Review of Genetics·Tim van Opijnen, Henry L Levin
Jan 5, 2021·Bioinformatics·Anna AbramovaJohan Bengtsson-Palme
Jun 6, 2020·Microbiological Research·Yaxing SuDehong Zheng

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