Question: contig with overlaps. how to circularize?
gravatar for jolespin
4.8 years ago by
United States
jolespin130 wrote:

if you have a contig with overlap in it, what is the best way to circularize a sequence?  Are there any tools that do this for you? I have CLC but I'm not sure how to do it in there. 

dna circular contig assembly genome • 2.5k views
ADD COMMENTlink modified 4.8 years ago by Philipp Bayer6.6k • written 4.8 years ago by jolespin130
gravatar for Philipp Bayer
4.8 years ago by
Philipp Bayer6.6k
Philipp Bayer6.6k wrote:

Give Criclator a try - it's made for using PacBio or nanopore reads, but if your contig already overlaps, maybe it'll work with "normal" read data too:



ADD COMMENTlink written 4.8 years ago by Philipp Bayer6.6k

Do you know if it adjusts the starting point of the linear representation of the contig if there's N-terminus ORF fragment in the 3'-end of the contig and C-terminus ORF fragment in the 5'-end of the contig? I don't have the time to read the paper right now. Anyway, nice find. I will definitely check this one out later.

ADD REPLYlink modified 4.8 years ago • written 4.8 years ago by 5heikki8.7k
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