Tool for Contig joining on overlaps ?

Question

[perrettony]

Hi there,

For my first post on BioStars, I would like to ask a question.

I used an assembly pipeline based on SOAP-denovo to produce a few thousand contigs from Illumina PE-reads.

I noticed that some contigs overlap on the 5' or 3' ends by just a few BPs (4-25 nt) . When I compare to sequences from a close species I can see that it really makes sense to join them.

I tried SSPACE but it makes scaffolds full of Ns. I just need to do contig joining one terminal overlaps, any idea ?

Thank you for suggestions.

Tony

Answer 1

[Prakki Rama]

You can try running CAP3, check if option overlap length cutoff (-o) is useful to you.

[perrettony]

Thanks for your answer.

The concept of CAP3 is good, but it cannot find overlaps shorter than 15 bp. Is there any tool more "sensitive" ?

[jeccy.J]

I used cap3 as you suggested. So after denovo assembly if we used cap3 then we can reduce the number of contig and minimize the gap also ??? what's your idea ??? or else i am missing something??