Question: Why is there no pipeline (windows based) for pangenome analysis of eukaryotes?
gravatar for Bioinfo_learner
7 weeks ago by
Bioinfo_learner20 wrote:

EUPAN is a pipeline I came across which basically just lists down all linux based softwares to be installed separately and run killing the purpose of there are many bacterial pangenome analysis pipelines on a more easier click to go way such as BPGA.

ADD COMMENTlink written 7 weeks ago by Bioinfo_learner20

Windows is not friendly to pipelines or scripting - not as friendly as Unix/Linux at least.

ADD REPLYlink written 7 weeks ago by RamRS28k

Sure but we do have alot of 1 or 2 click options of BPGA and such pipelines for prokaryotes.

ADD REPLYlink written 6 weeks ago by Bioinfo_learner20

Sure, but prokaryote algorithms are a lot less computationally intense IMO. I don't see the point of point-and-click software for computationally intensive algorithms, especially for Windows. Can you make the case for creating a Graphical Interface for BWA or STAR or HaplotypeCaller?

ADD REPLYlink written 6 weeks ago by RamRS28k

I totally second your opinion! As much as I enjoy working on Linux, there are many people new to Bioinformatics with little to no knowledge of the software side. IMO a graphical interface that lets you perform the similar steps specifically in case of pangenome analysis (which primarily has blast alignments and clustering) would be helpful for a lot of new learners. As for BWA/STAR etc., there is an option of Galaxy interface which returns the desired results even if it is not run on linux/unix platform.

ADD REPLYlink written 6 weeks ago by Bioinfo_learner20

I'm guessing there is software out there that does this. MacVector is the only GUI based software that I have used, and these kind of software definitely have their use. One could probably find such software with a lot of Googling. If you're looking to create such a point-and-click software, I wish you all the best. Just make sure there's sufficient demand for it.

ADD REPLYlink written 6 weeks ago by RamRS28k
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