Hi all,

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,
I'd suggest Unicycler. From my experience it sometimes helps to assemble the long reads first using Flye and feed that as a pre-assembly back into Unicycler using both short and long reads.
Tricycler would also be an interesting option with various rounds of short read polishing afterwards - but no experience so far with that.