Hi all,
I am currently setting up two QIAseq PRO targeted DNA panels for the analysis of DNA from human FFPE samples in my lab. We are using an Illumina MiSeq platform for NGS.
I want to detect SNV, small indels and CNV in a clinical setting.
We have two options for bioinformatics analyses: Use Qiagen products or build a pipeline in house. We already tried the latter but are hampered by lack of resources.
Qiagen’s solutions include either their software CLC Workbench, which is expensive (about 11 K) or using their online services for secondary analysis (QCI Secondary).
Qiagen warned me that their workflow templates for the panels in CLC Workbench are merely a starting point and require optimization.
Instead of trying this myself, they recommend their services in implementing a secondary analysis pipeline (QCI Secondary), which is also expensive (about 12 K per panel plus 500 for adding primer sets without further optimization, plus initial setup).
Do you have any experience in optimizing workflow templates for off-the-shelf targeted DNA panels in the CLC Workbench software?
How complicated is this?
Did you ever update your analysis templates after adding primer sets to off-the-shelf targeted DNA panels?
Do you have any insights on CLC Workbench versus QCI Secondary?
We chose these panels because some of our most influential doctors have used them before and strongly recommended them.
Qiagen initially presented the panels and software as ready to use and mentioned the immense costs for the software and optimization later.
I am still taken aback by the fact that Qiagen was not candid about the costs when they sold the panels.
Since we have already produced quite a lot of raw data switching to another vendor and starting over is probably not an option.
I am inclined to using their services (QCI Secondary and maybe QCI I for interpretation) instead of trying to figure things out on CLC Workbench myself, but I am unsure whether they are overcharging.
Unfortunately, I cannot judge this myself. I have not worked with this software yet.
Thanks for any insights you might have.
I am currently setting up two QIAseq PRO targeted DNA panels for the analysis of DNA from human FFPE samples in my lab. We are using an Illumina MiSeq platform for NGS.
I want to detect SNV, small indels and CNV in a clinical setting.
We have two options for bioinformatics analyses: Use Qiagen products or build a pipeline in house. We already tried the latter but are hampered by lack of resources.
Qiagen’s solutions include either their software CLC Workbench, which is expensive (about 11 K) or using their online services for secondary analysis (QCI Secondary).
Qiagen warned me that their workflow templates for the panels in CLC Workbench are merely a starting point and require optimization.
Instead of trying this myself, they recommend their services in implementing a secondary analysis pipeline (QCI Secondary), which is also expensive (about 12 K per panel plus 500 for adding primer sets without further optimization, plus initial setup).
Do you have any experience in optimizing workflow templates for off-the-shelf targeted DNA panels in the CLC Workbench software?
How complicated is this?
Did you ever update your analysis templates after adding primer sets to off-the-shelf targeted DNA panels?
Do you have any insights on CLC Workbench versus QCI Secondary?
We chose these panels because some of our most influential doctors have used them before and strongly recommended them.
Qiagen initially presented the panels and software as ready to use and mentioned the immense costs for the software and optimization later.
I am still taken aback by the fact that Qiagen was not candid about the costs when they sold the panels.
Since we have already produced quite a lot of raw data switching to another vendor and starting over is probably not an option.
I am inclined to using their services (QCI Secondary and maybe QCI I for interpretation) instead of trying to figure things out on CLC Workbench myself, but I am unsure whether they are overcharging.
Unfortunately, I cannot judge this myself. I have not worked with this software yet.
Thanks for any insights you might have.