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2.2 years ago
Kumar
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170
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!
Pilon does not circularize the assembly. After polishing you should try Circlator or Berokka.
ps. bacteria not always have a circular chromosome
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.
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