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

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 variety of species, (ii) Illumina reads from 5 isolates for which finished genome sequences

SUBMITTER: Hawkey J 

PROVIDER: S-EPMC4558774 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature