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

BMC Genomics
Jane HawkeyKathryn E Holt

Abstract

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. 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 97 % 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 able to correctly detect insertions fo...Continue Reading

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Citations

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Datasets Mentioned

BETA
ERR343331
AY758396
CP010781
X17348

Methods Mentioned

BETA
PCR
Illumina sequencing

Software Mentioned

TIF
MindTheGap
RAxML
SAMTools
nucleotide BLAST
RelocaTE
BreakDancer
BLAST
Annot
ISfinder BLAST

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