MicrobeTrace and its Alternatives

MicrobeTrace is a tool that's trying to make a particular type of analysis easier. There are some other, similar tools trying to accomplish the same thing. Let's talk about a few of them, and compare pros and cons:

HIV-TRACE

HIV-TRACE, or HIV-TRAnsmission Clustering Engine is a software package designed to consume a FASTA file containing HIV sequences, compute a genetic distance matrix (using the tn93 algorithm), label pairwise links between sequences according to whether they fall below a predefined threshold, and output the results.

If this sounds vaguely familiar, that's because it's almost exactly what MicrobeTrace does. And there's a good reason for this: MicrobeTrace was originally a wrapper for HIV-TRACE. However, circa Spring of 2017, we realized that the executable environment containing all of HIV-TRACE's dependency stack was unwieldy and difficult to use. To solve this problem, we replicated the data workflow in Javascript, enabling MicrobeTrace to perform all of the above steps in a single environment. This transition came at a performance cost. Because HIV-TRACE can access the machine on which it's running more-or-less directly, it can perform certain operations much more rapidly.

MicrobeTrace brings other substantial advantages to the table. Instead of a complex (error-prone) installation process with multiple dependencies, MicrobeTrace is a website. To load it, simply visit the URL. Furthermore, HIVTRACE is used on the command-line, which is confusing and difficult (if not frightening) for non-technical users. MicrobeTrace is a Graphical User Interface which is designed to guide the user gently through every step of the process. Finally, MicrobeTrace's output is also graphical. MicrobeTrace shows you a network, where HIVTrace merely outputs a statistical description of it, and a network file (which MicrobeTrace can open, BTW).

DataMonkey and Secure HIV-TRACE

While MicrobeTrace sought to make HIV-TRACE analysis available through the Browser, DataMonkey and Secure HIV-TRACE both sought to make HIV-TRACE available through a server.

GHOST

GHOST, or the global hepatitis outbreak and surveillance technology

MicroReact

MicroReact

NextFlu and NextStrain

NextFlu and NextStrain

NextHIV

NextHIV

...which brings us back to MicrobeTrace

MicrobeTrace is the only platform which pairs a premium on ease-of-use with data security guarantees. For the non- or semi-technical analyst, it's more feature-full than any other molecular epidemiology platform presently available.