Update on the Broad Viral Group

[Daniel Park]

Hi Broad viral tool users,

I'm newish to this list and this is my first time posting, but I thought it'd be helpful to connect with you and give an update on recent changes over the past few years. Sorry I haven't done this earlier.

The Broad Viral Genomics team has undergone various changes in personnel, funding, and mandated priorities, starting around 2013. This resulted in slightly less emphasis on novel algorithmic development, but especially much less of an ability to maintain and support some of the older computational tools that had been previously developed (e.g. Vicuna, ATHLATES, etc).

The Broad Viral team is working on a number of software projects relevant to our priorities, but as we release those, they will be released on GitHub, which comes with a better mechanism for questions, problems, bug reports, and user support issues. Of the previously released software tools, V-Phaser2 is the only one we are keeping alive in some way (for now), and that's mostly in the form of the BioConda package to assist with compile-time troubles, as well as custom output parsing and filtering scripts that we find useful (see the viral-ngs project referred to in an earlier thread). We're actively in the process of replacing V-FAT with something more appropriate to our own needs.

Regarding this email list: I should note that while new members, such as myself, can join this google group at any time, it currently has no administrators or moderators (all email accounts for previous admins no longer exist) and this is essentially an orphaned Google group (or "zombied"--it can't be killed by anyone). There are probably better ways to reach us anyway, including GitHub (which a few folks have already done with V-Phaser2 questions). Or please feel free reach out to me directly via email.

However, before declaring this email list officially defunct, I'd like to take the opportunity to ask this community about which of the older tools you continue to find essential / useful for your own research and would have a hard time finding alternatives for. Some of these tools seem to address older problems that are less applicable to current methodologies, and some seem to have been supplanted by newer methods by other groups. But if some are currently filling an otherwise unmet need, I'd love to know about that.

Danny Park

--

Daniel J. Park, PhD

Group Leader, Viral Computational Genomics

Broad Institute of MIT and Harvard

Tel: +1-617-714-8526

dp...@broadinstitute.org

http://www.broadinstitute.org/bios/daniel-park