I have a bacterial genome that I know has an approximate size of 7.3m. I have both short-reads (Illumina) and long-reads (Pacbio). Sequencing showed good coverage. I tried to assemble these data using SPAdes, Flye or Canu but I can not obtain a circular chromosome contig. I know there is plasmid contigs in this genome but the best assembly I got was with Flye (and rounds of Pilon) with a total of 8 contigs.
Do you know another assembler tool that I can use? Do you have any advices on how should I perform this assembly?
Thank you very much for your help,
As hybrid assembler you could try Unicycler
You can try circulator to circularize the assembly.