bacterial genome circularization
0
0
Entering edit mode
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
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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
0
Entering edit mode

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

Login before adding your answer.

Traffic: 1005 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6