bacterial genome circularization

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4.3 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

genome bacteria circlator circularization • 1.3k views

ADD COMMENT • link 4.3 years ago by star715 ▴ 40

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I suggest you consider that you may not have enough data to circularize the genome.

ADD REPLY • link 4.3 years ago by Mensur Dlakic ★ 27k

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Were you able to assemble a single Contig (excluding contigs which might correspond to episomal DNA)?

Is there a reference for this bacteria?

ADD REPLY • link 4.3 years ago by Joe 21k

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Yeah I could assemble into a single contig. And yes, it has a reference.

ADD REPLY • link 4.3 years ago by star715 ▴ 40

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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.

ADD REPLY • link 4.3 years ago by Joe 21k

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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?

ADD REPLY • link 4.3 years ago by chernouhov sergey ▴ 50

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