Merging two split contigs

Question

[s.kyungyong64]

Hi all,

I have contigs assembled by Canu. While annotating the contigs, I realized that contig A and contig B are actually continuous but split as two different contigs. The end of contig A is overlapping with the end of contig B with 100% ID over a significant length.

contigA        >.......................[Overlapping region]

contigB                                [Overlapping region]..............>

I need to check if other contigs are split like this case. But it's hard to make such an alignment with alignment tools due to their algorithms. Does anyone know the best way to identify such contigs (other than BLAST) and make a proper alignment?

Thanks,

Answer 1

[maxwhjohn1988]

Just an idea - not sure whether it would work - but you could try providing your contigs to Canu as long read sequences to be assembled, and see if it stitches those which overlap, as you described, back together. I'm trying to think of reasons why this could happen - might there have been some mate-pair information which indicated to the assembler that these sequences were not in fact contiguous with each other?