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.
Give Circlator 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:
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.
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