Question: Clipping contig overlaps
gravatar for misaghb
5.6 years ago by
United States
misaghb20 wrote:

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?

alignment assembly • 1.6k views
ADD COMMENTlink written 5.6 years ago by misaghb20

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?

ADD REPLYlink written 5.6 years ago by Rayan Chikhi1.4k

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.

ADD REPLYlink modified 5.6 years ago • written 5.6 years ago by misaghb20

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.

ADD REPLYlink written 5.6 years ago by Rayan Chikhi1.4k
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