Hi everyone, I am trying to analyse the whole genome sequences of Pseudomonas strains generated from Illumina Next Generation Sequencing platform and my aim is to identify insertions of specific family of transposons (around 10 kb) in the genome and retrieve it. I have access to CLC genomics Workbench. Can someone suggest me any method to find the sequences. P.S- I have tried to assemble the sequences but I could only obtain contigs less than 100 Kb. Thank you
If you are limited to using CLC then you should contact CLC tech support for assistance. Assuming your libraries are good quality and you have enough coverage, CLC should be able to assemble the genome in larger sizes than what you got. Have you tried to align the data to the reference already available?