I've build some contigs from using unmapped reads. Now, what I want to do is to see if any of those contigs can be included in the reference chromosomes. I've paired end reads and I was thinking about mapping and doing scaffolding with those reads than one end maps to a denovo contig and the other to reference chromosome... But I'm not sure about if this is a correct way to do it and also what software could I use for this...something like SGA?
I hope it is somehow clear!
Thanks in advance
Just to add to Istvan's answer, if you want to also compare your contigs to a reference (in addition to scaffolding) you can use mummer or bwa-mem. If you are trying to achive some kind of gap-filling using a reference, take a look at the PAGIT pipeline. Within the PAGIT pipeline there is a program called ABACUS that will orient your contigs relative to the reference, and IMAGE (also part of PAGIT) can be used to fill the gaps.
You can try tools like SSPACE that was designed to help scaffold contigs with paired end reads