I have question, as this is usually not my field of working at all! I'm used to work with bacterial genomes, but I have small project including Chlamydomonas mutants then I would like to ask experts what they are doing to do my "best". I have 7 strains of Chlamydomonas mutants with they Illumina reads and I need to find potential transposons inside their genomes (which is NOT in the WT). I was wondering what is the best strategy :

1. mapping the reads with bwa-mem against the new reference genome of Chlamydomonas (v6) but with (if I understood well) the huge diversity of strains, will I be able to see the transposons?
2. doing denovo assembly with spades or soapdenovo and mapping the contig against the reference genome after with mummer?

I have some preference for number 2 but I'm afraid denovo assembly of this kind of genome with short reads (30X) will be a disaster

Thanks for your help!