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How to make circularize genome assembly after polishing

Hi, I have assembled a bacterial genome using Flye assembler. In the results, it say the assembly is circulated since it it bacterial genome.

llumina reads have much higher per-base accuracy than Nanopore reads so I mapped the Illumina read sets to the assembly (generated by Flye) using a short-read aligner called BWA-MEM. Then I used one round Pilon to polish the assembly.

My question is that after polishing using Pilon, is the assembly still circulated or again do I need to do circularize the assembly. If I need to perform circularize the assembly again after polishing please let me know how to circularize (any pipeline) the assembly.

Thank you!

assembly genome flye assember pilon
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updated by andres.firrincieli andres.firrincieli • written by Kumar Kumar

Pilon does not circularize the assembly. After polishing you should try Circlator or Berokka.

ps. bacteria not always have a circular chromosome

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written by andres.firrincieli andres.firrincieli

Thank you for reply. The assembly from Flye assembler seems circularize but after using Circlator the results indicate circularize: No. Even one of my assembly is confirmed circularize using Unicycler and once I use Circlator for this assembly it shows circularize: No. I am not sure if the Circlator is correct.

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written by Kumar Kumar

without start-end overlap, Circlator cannot circularize the chromosome. Compared to other assemblers Flye usually provides contigs with contiguity near to 100%. If the contiguity is exactly 100% or lower this indicates that the contig does not contain duplicated sequence via start-end overlap.

Use Bandage to look at the assembly graph provided by Flye, and check if the Chromsomome is linear or circular.

Let me know

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written by andres.firrincieli andres.firrincieli

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