I have assembled multiple bacterial genomes sequenced using Oxford Nanopore Minion (FLO-MIN106 flowcell) sequencer.
I have used Pomoxis, Unicycler assemblers to perform the genome assembly. Upon annotating the resultant fasta files of the genome assembly using RAST and PATRIC, I have observed the CDS number to be abnormally hight (Double in some cases) when compared to existing assemblies.
CDS ratio rages from 0.44 to 0.60 (Normal CDS ratio prescribed by NCBI ranges between 0.8 and 1.2).
How can I overcome this issue of abnormal CDS count issue. What is the way forward?
Thanking you all