Journal article

ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data

Jane Hawkey, Mohammad Hamidian, Ryan R Wick, David J Edwards, Helen Billman-Jacobe, Ruth M Hall, Kathryn E Holt

BMC GENOMICS | BIOMED CENTRAL LTD | Published : 2015

Abstract

BACKGROUND: Insertion sequences (IS) are small transposable elements, commonly found in bacterial genomes. Identifying the location of IS in bacterial genomes can be useful for a variety of purposes including epidemiological tracking and predicting antibiotic resistance. However IS are commonly present in multiple copies in a single genome, which complicates genome assembly and the identification of IS insertion sites. Here we present ISMapper, a mapping-based tool for identification of the site and orientation of IS insertions in bacterial genomes, directly from paired-end short read data. RESULTS: ISMapper was validated using three types of short read data: (i) simulated reads from a varie..

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University of Melbourne Researchers

Grants

Awarded by National Health and Medical Research Council of Australia


Awarded by Victorian Life Sciences Computation Initiative (VLSCI)


Funding Acknowledgements

This work was supported by the National Health and Medical Research Council of Australia (Fellowship #1061409 to KEH; Project Grant #1043830 to KEH and RMH) and the Victorian Life Sciences Computation Initiative (VLSCI, #VR0082).