Hello to everybody,
I need to identify repetitive elements of 5 genotypes from the same species (a plant species that is not yet sequenced). For that, I have different datasets:
1) Illumina paired-end reads from these 5 species
2) BAC sequencing reads (I do not know the sequencing platform, but they are 300nt long) from only one genotype.
I hesitate what to do with the first step: assembly. My initial idea was doing de-novo assembly with SOAPdenovo or assembly with specific assemblers to identify repeats such as SWA. However, I do not know how to handle sequencing data from BACs or how to combine Illumina paired-end reads with reads from BACs.
What strategy would you do?
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