looking for resistance cassette in illumina reads of transducted strain

Question

[strepto94]

Hello, I have to fnid an integration kanamycin cassette in paired ends reads or corresponding scaffold. We know that an integration occurred, but it didn't took place at the expected locus. What could be the best option to find where it tookplace? I thought of blasting, however I guess that it will be hard taking into account that we have few reference genomes.

Please could you help me?

JF

[GenoMax]

You could do this a couple of ways. If you have enough sequence data you could try to assemble the genome and then find the contig with the kanamycin cassette with a blat/blast search. Or you could try to bin the reads containing kanamycin cassette using bbsplit.sh from BBMap suite. Then try and assemble those reads using a k-mer based aligner such as tadpole.sh again from BBMap suite (guide here). Then look at the reads (past the edge of kanamycin cassette) to see if you can identify where the insertion is located in the genome.