integron_gene_fetch is developed to get integron genes from metagenomic sequencing reads. It is capable of getting the integron mobile genes more efficiently, as these genes are extremely difficult to be detected in whole-genome assembly. By assembling the dataset and traces all potential paths between any two contigs that consist of recombination sites, the integron_gene_fetch tool is able to get more integron genes given a pre-determined set of recombination site sequences.
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Yu-Wei Wu, Mina Rho, Thomas G. Doak and Yuzhen Ye.
Oral spirochetes implicated in dental diseases are widespread in normal human subjects and carry extremely diverse integron gene cassettes.
Appl. Environ. Microbiol. August 2012 vol. 78 no. 15 5288-5296