Finding contaminant contigs in assembly

[mandar.bobade60]

Hi,

I have generated plant mitochondrial assembly for which I would like to find contamination from chloroplast as well as nuclear genome. I have also run BlastN using same species nuclear genome and chloroplast genome database, and now with results I have some alignments with multiple scaffolds generated.

My question is, if it is wise cutting down sequences from assembly which are having high identity with substantive e-value with subject sequences or I need to see some other criteria along with identity and e-value?

Any help would be highly appreciated...

[bastianwur]

What about the length?
Longer alignment > smaller one.