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3.2 years ago
star715 ▴ 40
I want to circularize bacterial genomes assembled via HGAP (from long reads obtained from pacbio sequencing). Circlator however fails to circularize it. What could be other options given I have only long reads?
Also, if there is some way to fix the performance by circlator (I am using default circlator all command), it would be very helpful. Thanks
I suggest you consider that you may not have enough data to circularize the genome.
Were you able to assemble a single Contig (excluding contigs which might correspond to episomal DNA)?
Is there a reference for this bacteria?
Yeah I could assemble into a single contig. And yes, it has a reference.
How do the ends of your sequence compare to the reference (is the reference a complete/closed genome?).
If the ends of your Contig haven't sequenced well, there may not be enough information in the permutation of the sequence to close it successfully.
May I see the input data? By the way, in my C++ lib CBioInfCpp there is a function for rough making circular string from a linear one, StrToCircular. But maybe there are some additional rules how to do?