Should I use contigs or the scaffolds for comparing illumina based de novo assembly with the reference genome?
Not sure if you question was answered. I would always work with scaffolds if generated them conservatively. Comparing them to the reference genome (like with abacas), you could find more likely differences in the synteny - but be aware that most of the assembly errors are due to scaffolding! Depending on the overall assembly quality, so if the scaffolds are significantly longer than the contigs (e.g. due to large insert size library), you might be able to order more against the reference and see some insertions, not in the reference.
I agree that if you look for differences in the genes, it does not make a difference
BTW, if you want to annotate an assembly similar to your reference, have a lot at RATT and for assembly improvement PAGIT: http://www.nature.com/nprot/journal/v7/n7/full/nprot.2012.068.html
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