Mar 10, 2015

ISMapper: Identifying insertion sequences in bacterial genomes from short read sequence data

BioRxiv : the Preprint Server for Biology
Jane HawkeyKathryn E Holt

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, direct from paired-end short read data. Results ISMapper was validated using three types of short read data: (i) simulated reads from a variety of species, (ii) Illumina reads from 5 isolates for which finished genome sequences were available for comparison, and (iii) Illumina reads from 7 Acinetobacter baumannii isolates for which predicted IS locations were tested using PCR. A total of 20 genomes, including 13 species and 32 distinct IS, were used for validation. ISMapper correctly identified 96% of known IS insertions in the analysis of simulated reads, and 98% in real Illumina reads. Subsampling of real Illumina reads to lower depths indicated ISMapper was reliable for average g...Continue Reading

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Mentioned in this Paper

Genome-Wide Association Study
Acinetobacter calcoaceticus
Uvaria baumannii
Genome
Amorphophallus baumannii
Genome Assembly Sequence
Cephalosporins
Site
Tracking
Reading Frames (Nucleotide Sequence)

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