Karen Davenport, LANL:
From Raw Reads to Trees: Whole Genome Single Nucleotide Polymorphisms Phylogenetics Across the Tree of Life
This presentation may win for longest title.
So Los Alamos National Laboratories (LANL) puts out lots of different bioinformatics tools with their more well known tools, from my perspective, being PhaME (bioRxiv paper), EDGE (NAR paper) and GOTTCHA (NAR paper).
I was a part of a group from WRAIR that tested their EDGE platform when it was originally being developed. While it has a lot of good software integrations (packaging up of open source software for pathogen detection, surveillance and other analyses), for me, 'black box' bioinformatics solutions always have their caveats. I see these 'all-in-one' answers as exploratory tools that require validation at the very least with other pipelines. Additionally, with the large software packages like EDGE, if there is no comprehensive manual or links to manuals of programs integrated into the system then I am suspicious of the 'default' settings and why they were set in that way. I've have had many a reviewer ask for justifications on my data analysis set ups and if you cannot justify your settings (default or not) then you don't understand what the analysis is really doing to your data. Perhaps I just have an innate distrust of machine default outputs.
To LANL and the EDGE team's credit this is posted on their readthedocs site for EDGE:
"While the design of EDGE was intentionally done to be as simple as possible for the user, there is still no single ‘tool’ or algorithm that fits all use-cases in the bioinformatics field. Our intent is to provide a detailed panoramic view of your sample from various analytical standpoints, but users are encouraged to have some insight into how each tool or workflow functions, and how the results should best be interpreted."
Like they read my mind...this is good advice for any tool(s) that you use.
