My guilty bioinformatics pleasure is using Geneious- it really is very good for messing around with viral genome sequences.
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Fit different niches, IMHO. CLC is much better suited to complex NGS microbial workflows, but is correspondingly more expensive. Geneious is great as a convenient graphical front end for some lightweight bioinformatic exploration.
This used to be true, but I actually think Geneious has that part covered too these days? Lots of good primary tools for assembly, mapping, cleaning, etc, followed by a suite of analysis tools. My main gripe with Geneious is that it crams everything into a SQL database...
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I haven't messed with it in a few versions, back when they introduced a rudimentary workflow engine. It's great for what it is. My view might have been tempered by the fact that I was stress testing it on larger genome assemblies and seeing how it handled metagenomic samples.
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I haven’t actually tried workflows in Geneious, but they’re there. As soon as a workflow (or anything n>1) is involved, I switch to the terminal
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