Hi there,
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
2 answers
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.
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