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TRANSIT - A Software Tool for Himar1 TnSeq Analysis

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  • Michael A DeJesus
  • Chaitra Ambadipudi
  • Richard Baker
  • Christopher Sassetti
  • Thomas R Ioerger

Abstract

TnSeq has become a popular technique for determining the essentiality of genomic regions in bacterial organisms. Several methods have been developed to analyze the wealth of data that has been obtained through TnSeq experiments. We developed a tool for analyzing Himar1 TnSeq data called TRANSIT. TRANSIT provides a graphical interface to three different statistical methods for analyzing TnSeq data. These methods cover a variety of approaches capable of identifying essential genes in individual datasets as well as comparative analysis between conditions. We demonstrate the utility of this software by analyzing TnSeq datasets of M. tuberculosis grown on glycerol and cholesterol. We show that TRANSIT can be used to discover genes which have been previously implicated for growth on these carbon sources. TRANSIT is written in Python, and thus can be run on Windows, OSX and Linux platforms. The source code is distributed under the GNU GPL v3 license and can be obtained from the following GitHub repository: https://github.com/mad-lab/transit

Suggested Citation

  • Michael A DeJesus & Chaitra Ambadipudi & Richard Baker & Christopher Sassetti & Thomas R Ioerger, 2015. "TRANSIT - A Software Tool for Himar1 TnSeq Analysis," PLOS Computational Biology, Public Library of Science, vol. 11(10), pages 1-17, October.
    • Handle: RePEc:plo:pcbi00:1004401
    DOI: 10.1371/journal.pcbi.1004401
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    1. Aldert Zomer & Peter Burghout & Hester J Bootsma & Peter W M Hermans & Sacha A F T van Hijum, 2012. "ESSENTIALS: Software for Rapid Analysis of High Throughput Transposon Insertion Sequencing Data," PLOS ONE, Public Library of Science, vol. 7(8), pages 1-9, August.
    2. Justin R Pritchard & Michael C Chao & Sören Abel & Brigid M Davis & Catherine Baranowski & Yanjia J Zhang & Eric J Rubin & Matthew K Waldor, 2014. "ARTIST: High-Resolution Genome-Wide Assessment of Fitness Using Transposon-Insertion Sequencing," PLOS Genetics, Public Library of Science, vol. 10(11), pages 1-15, November.
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    1. Di Qu & Peng Ge & Laure Botella & Sae Woong Park & Ha-Na Lee & Natalie Thornton & James M. Bean & Inna V. Krieger & James C. Sacchettini & Sabine Ehrt & Courtney C. Aldrich & Dirk Schnappinger, 2024. "Mycobacterial biotin synthases require an auxiliary protein to convert dethiobiotin into biotin," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    2. Samuel Miravet-Verde & Rocco Mazzolini & Carolina Segura-Morales & Alicia Broto & Maria Lluch-Senar & Luis Serrano, 2024. "ProTInSeq: transposon insertion tracking by ultra-deep DNA sequencing to identify translated large and small ORFs," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    3. Kaj M. Kreutzfeldt & Robert S. Jansen & Travis E. Hartman & Alexandre Gouzy & Ruojun Wang & Inna V. Krieger & Matthew D. Zimmerman & Martin Gengenbacher & Jansy P. Sarathy & Min Xie & Véronique Dartoi, 2022. "CinA mediates multidrug tolerance in Mycobacterium tuberculosis," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    4. Jeffrey A. Freiberg & Valeria M. Reyes Ruiz & Brittney D. Gimza & Caitlin C. Murdoch & Erin R. Green & Jacob M. Curry & James E. Cassat & Eric P. Skaar, 2024. "Restriction of arginine induces antibiotic tolerance in Staphylococcus aureus," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    5. Henri Voedts & Sean P. Kennedy & Guennadi Sezonov & Michel Arthur & Jean-Emmanuel Hugonnet, 2022. "Genome-wide identification of genes required for alternative peptidoglycan cross-linking in Escherichia coli revealed unexpected impacts of β-lactams," Nature Communications, Nature, vol. 13(1), pages 1-14, December.

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