Assembly Of Illumina

Question

[raj.gzra]

hello everyone i have a genome which is already assembled and it has contamination so we remove contamination from this genome. and we again resequenced the genome but yet we did not assemble. both data is of same species. one is assembled genome data in form of scaffold. and another is raw reads of illumina. so i want to know does it possible that we can assemble these raw reads with already assembled genome? or is it good to do like that? or if it is good then why?
thank you in advance..

[Chris Fields]

It might be better if you could mention what you want to do (e.g. maybe what questions you want answered). For instance, if you only care about differences between the reference genome and your sample, you could align reads and call variants.