Could anyone tell me how I could assemble my own karyotype file for circos plot? I am working on a bacteria project. The species is called Candidatus Kuenenia stuttgartiensis, which belongs to phylum/Clade Planctomycetes. I could not find the data from stuttgartiensis in UCSC table. I googled Ca. K stuttgartiensis's genome as well but found nothing. I combined all the contigs from this source and use it as the reference genome.
I have finished mapping through bwa, formatting through Samtools and merging overlapping sequences and generating coverage report through BEDTools.
Thanks in advance!