Clipping contig overlaps
Is there any tool to automatically clip the flanking sub-sequences of contigs (beginning and end of each contig) that overlap with other contigs? Is there any command-line key in running well-known assemblers (Velvet, SOAPdenovo, ABySS, Minia, ...) to output overlap-free contigs?
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I'm not aware of one.. such a tool would need to overlap the contigs again to recreate the assembly graph.
What's the purpose? is it because you're concerned with the sequence redundancy of (k-1) nucleotides at each overlap?
Thanks Rayan. Actually I want to perform some sort of automatic scaffolding (my own program) and before that I want to make sure input contigs are not overlapped hence the distance between any two contigs would be a non-negative integer number.
I see.
If your goal is to perform scaffolding, it might help you to know which contigs are overlapping.. A predicted negative gap + contigs overlapping by k-1 is stronger evidence for correct scaffolding than just one of the two.