This website is intended to be a community forum for people using Nextstrain. We’re very interested to help public health and academic groups run Nextstrain analyses and share them (publicly or privately). The goal is to connect the community with each other and the core Nextstrain team in order to share information and ideas and offer help. We can all learn together as part of a larger community of practice.
We also hope discussion here will help identify what Nextstrain is missing and guide future development directions. If you have ideas here, please share!
If this is your first time here, welcome! Please feel free to introduce yourself in the replies below and make a new topic in General describing how you’re using (or would like to use) Nextstrain. If you need help using Nextstrain, make a new topic in Help and Getting Started and we’ll do our best to help out.
Questions are answered by a combination of the Nextstrain team and the community. For the Nextstrain team, time to read, investigate, and respond to questions varies day to day, week to week, etc. and also by the knowledge/expertise of individual team members. Some questions are easier and quicker to answer than others; some require more thought and time. If a question of yours goes unanswered for a while, sometimes rephrasing or adding more information in a reply can help. It certainly doesn’t hurt, and at the least, it bumps the question back into people’s notifications in case it fell through the cracks.
I’ll start the introductions! My name is Thomas Sibley, and I’m a member of the Bedford Lab. I work as a lead software engineer on Nextstrain, the greater Seattle Coronavirus Assessment Network study (SCAN), and the preceding Seattle Flu Study. I’m particularly interested in making Nextstrain’s toolset easier to use, via things like the Nextstrain CLI and Nextstrain Groups.
Hi all! My name is John Huddleston. I’m a PhD candidate in the Bedford Lab through the University of Washington’s Molecular and Cell Biology Program. I develop methods to improve long-term forecasts of viral evolution (specifically influenza A/H3N2). I am also a Nextstrain developer and contribute most substantially to command line components like augur.
Hello! My name is Lynette Gumbleton and I am with Wyoming Public Health Laboratory. I have been charged with task of creating a NextStrain local build for Wyoming. I am looking for help getting started!
My name is Alex Rubinsteyn and I’m a new PI at UNC. I have worked primarily on cancer vaccines and machine learning for immunology but, like many people, I have taken an interest in virology this year. I’m currently collaborating with other folks at UNC on the sequencing surveillance of SARS-CoV-2 samples.
Hello! My name is Adam Retchless. I am a bioinformatician at the Centers for Disease Control and Prevention. I had been working on bacterial meningitis, but was recently brought on to the COVID-19 response. For the moment, I am mainly concerned with understanding the nomenclature used by NextStrain, and how it is used to track variants of concern. In the future, I hope to have opportunities to use the analysis and visualization features of NextStrain. It’s an awesome website – thanks so much for building it!
Hi! My name is Julie Campbell and I am a Director of Labs in Introductory Biology at the University of Kansas. The pandemic has meant a move to remote learning for the introductory labs I oversee. One topic we cover is the biology of SARS-CoV-2. Students have completed a two part lab on Systematics prior to doing the SARS-CoV-2 lab as well as a lab on influenza. SARS-CoV-2 lab, they are instructed to look at the Next Strain website, but I don’t have any specific activities associated with it. Does anyone have suggestions on some questions or activities that introductory level undergraduates could do using Next Strain? -THANKS!
Hi, my name is Cheryl Davis. I manage the COVID-19 PCR diagnostic lab for Tuskegee University. I want to use Nextstrain to correlate viral targets patterns with variants in the database. We are not sequencing, so the information on how the mutations affect diagnostic testing is important and very valuable.
Hello everyone
My name is Sikandar Azam and I am a PhD candidate in the Department of Virology at Tohoku University Japan. I am working on Respiratory Viruses (especially Influenza virus and RSV) and I am using Nextstrain to understand how the viruses are circulating/evolving and tracking the virus spread. The next strain is really helpful in this regard, Thank you for building this amazing platform
Hi, my name is Brian Foley. I am the PI of the HIV Databases at LANL. I have been viewing the NextStrain SARS-CoV-2 trees a bit since 2019 to follow the evolution of that virus. And a few years ago, I used Augur and Auspice at the Interactive Tree of Life site, to create some HIV-1 trees. We are now making a “group” page here at NextStrain to put up some HIV-1 M group trees, and later we may add a tree of a wider variety of lentiviruses.
My name is Sergio Ortega Del Campo, PhD student at the University of Malaga. I have seen that in your page “Latest global SARS-CoV-2 analysis” you have a panel that shows the diversity observed in the whole genome of SARS-CoV-2 or in a selectable CDS. I would like to know what software you have used to create that kind of graph, as I would like to make one with my data. Thank you very much and congratulations for the work you are doing.
@Sergio, the “Entropy” panel contents is calculated and rendered in our in-house software called Auspice. Auspice is a web application that you see when viewing specific pathogens on nextstrain.org. Auspice takes a phylogenetic tree in Auspice JSON v2 format and renders the tree, along with entropy panel, world map and other panels.
In order to create the entropy graph you’ll need to build a tree in Auspice JSON v2 format from your data. In Nextstrain organization this is typically done using Augur and other tools in a Snakemake workflow.
All our programs are open-source, so if you are into programming, you might also be able to implement the entropy graph yourself, using this code from Auspice as inspiration:
Hello! My name is Rishi Graham. I am a project scientist at University of California San Diego
Health. My background is in applied math, bayesian statistics, and computer science, but I find
myself in a bioinformatics-adjacent role the last couple years. We have been using nextstrain and some
associated sites (e.g., Emma Hodcroft’s CoVariants site) for SARS-CoV-2
situational awareness. These tools are very well designed, clear to use, and transparent. Kudos to
the team, and thank you for the good work!
Please feel free to introduce yourself in the replies below and make a new topic in General describing how you’re using (or would like to use) Nextstrain. If you need help using Nextstrain, make a new topic in Help and Getting Started and we’ll do our best to help out.
My name is Thomas Sibley, and I’m a member of the Bedford Lab. I work as a lead software engineer on Nextstrain, the