Question: contig with overlaps. how to circularize?
0
gravatar for jolespin
3.7 years ago by
jolespin120
United States
jolespin120 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 • 1.9k views
ADD COMMENTlink modified 3.7 years ago by Philipp Bayer6.0k • written 3.7 years ago by jolespin120
1
gravatar for Philipp Bayer
3.7 years ago by
Philipp Bayer6.0k
Australia/Perth/UWA
Philipp Bayer6.0k 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:

Paper: http://biorxiv.org/content/early/2015/07/30/023408

Homepage: http://sanger-pathogens.github.io/circlator/

ADD COMMENTlink written 3.7 years ago by Philipp Bayer6.0k

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 3.7 years ago • written 3.7 years ago by 5heikki8.4k
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