Dear @janka2012 ,
I have discovered digIS to be an intriguing tool and have commenced utilising it. Nevertheless, some questions have emerged.
In the course of executing Prodigal-based annotators, including Bakta and Prokka (both of which are effective annotators), it has been observed that the transposase CDSs yielded do not align with the anticipated IS coordinates. Indeed, there is a notable discrepancy in the coordinates. Upon manual examination, it became evident that the predicted IS was fragmented into two Bakta-annotated coding sequences (CDSs).
This prompted further investigation, which revealed that the ORF/CDS assignment is a crucial step, as it can vary between tools. Additionally, the assignment is highly dependent on the quality and assembly (fragmentation) of the genome. Consequently, it would be beneficial to ascertain whether digIS is suitable for working with draft genomes that have between 50 and 300 contigs.
Your insights on this matter are greatly appreciated.
Best regards,
Benjamin
Dear @janka2012 ,
I have discovered digIS to be an intriguing tool and have commenced utilising it. Nevertheless, some questions have emerged.
In the course of executing Prodigal-based annotators, including Bakta and Prokka (both of which are effective annotators), it has been observed that the transposase CDSs yielded do not align with the anticipated IS coordinates. Indeed, there is a notable discrepancy in the coordinates. Upon manual examination, it became evident that the predicted IS was fragmented into two Bakta-annotated coding sequences (CDSs).
This prompted further investigation, which revealed that the ORF/CDS assignment is a crucial step, as it can vary between tools. Additionally, the assignment is highly dependent on the quality and assembly (fragmentation) of the genome. Consequently, it would be beneficial to ascertain whether digIS is suitable for working with draft genomes that have between 50 and 300 contigs.
Your insights on this matter are greatly appreciated.
Best regards,
Benjamin