Parts of a whole

Nextstrain is made up of many different parts that all work together. Two core parts are Augur and Auspice.

digraph { graph [ rankdir=LR, ]; node [ shape=box, style="rounded, filled", fontname="Lato, 'Helvetica Neue', sans-serif", fontsize=12, height=0.1, colorscheme=paired10, ]; edge [ arrowhead=open, arrowsize=0.75, ]; Augur [fillcolor=1, color=2]; Auspice [fillcolor=3, color=4]; Augur -> Auspice; }

Augur is a series of composable, modular bioinformatics tools. We use these to create recipes for different pathogens and different analyses, which can be reproduced given the same input data and replicated when new data is available.

graph { graph [ ranksep=0.25, ]; node [ shape=box, style="rounded, filled", fontname="Lato, 'Helvetica Neue', sans-serif", fontsize=12, height=0.1, colorscheme=paired10, fillcolor=1, color=2, ]; edge [ arrowhead=open, arrowsize=0.75, ]; Augur -- ellipsis1 [style=invis]; ellipsis1 [label="…", shape=plain, style=""]; Augur -- {filter, align, tree, refine, export}; Augur -- ellipsis2 [style=invis]; ellipsis2 [label="…", shape=plain, style=""]; }

Auspice is a web-based visualization program, to present and interact with phylogenomic and phylogeographic data. Auspice is what you see when, for example, you visit nextstrain.org/mumps/na.

../_images/mumps.png

Auspice displaying Mumps genomes from North America.

Datasets are produced by Augur and visualized by Auspice. These files are often referred to as JSONs colloquially because they use a generic data format called JSON.

digraph { graph [ rankdir=LR, ]; node [ shape=box, style="rounded, filled", fontname="Lato, 'Helvetica Neue', sans-serif", fontsize=12, height=0.1, colorscheme=paired10, ]; edge [ arrowhead=open, arrowsize=0.75, ]; Augur [fillcolor=1, color=2]; Auspice [fillcolor=3, color=4]; jsons [label=< Dataset <FONT POINT-SIZE="10"> <BR ALIGN="LEFT"/>- mumps_na.json <BR ALIGN="LEFT"/>- mumps_na_root-sequence.json </FONT> >]; Augur -> jsons -> Auspice; }

Builds are recipes of code and data that produce these datasets.

digraph { graph [ ranksep=0.25, ]; node [ shape=box, style="rounded, filled", fontname="Lato, 'Helvetica Neue', sans-serif", fontsize=12, height=0.1, colorscheme=paired10, ]; edge [ arrowhead=open, arrowsize=0.75, ]; subgraph Augur { graph [rank=same]; node [fillcolor=1, color=2]; filter -> align -> tree -> refine -> export; } Dataset; Auspice [fillcolor=3, color=4]; export -> Dataset; Dataset -> Auspice; subgraph inputs { graph [rank=same]; sequences [label="sequences.fasta"]; metadata [label="metadata.tsv"]; } sequences -> filter; metadata -> filter; }

Builds run several commands and are often automated by workflow managers such as Snakemake, Nextflow and WDL. A workflow bundles one or more related builds which each produce a dataset for visualization with Auspice.

As an example, our core workflows are organized as Git repositories hosted on GitHub. Each contains a Snakemake workflow using Augur, configuration, and data.

digraph { graph [ fontname="Lato, 'Helvetica Neue', sans-serif", fontsize=12, ] node [ shape=box, style="rounded, filled", fontname="Lato, 'Helvetica Neue', sans-serif", fontsize=12, height=0.1, colorscheme=paired10, ]; rankdir=LR subgraph cluster_0 { label = "Zika workflow"; build0 [width=1, label="Zika build"] dataset0 [width=1, label="dataset"] } subgraph cluster_1 { label = "SARS-CoV-2 workflow"; build1 [width=1, label="Global build"] build2 [width=1, label="Africa build"] build3 [width=1, label="Europe build"] dataset1 [width=1, label="dataset"] dataset2 [width=1, label="dataset"] dataset3 [width=1, label="dataset"] ellipses1 [width=1, label="...", penwidth=0, fillcolor="white"] ellipses2 [width=1, label="...", penwidth=0, fillcolor="white"] } build0 -> dataset0 build1 -> dataset1 build2 -> dataset2 build3 -> dataset3 { edge[style=invis] dataset0 -> build1 // arrange clusters on same row ellipses1 -> ellipses2 } }

nextstrain.org is a web application to host and present the core pathogen datasets maintained by the Nextstrain team, as well as datasets published to Nextstrain Groups and community pages which are maintained and shared by many other people. The website incorporates a customized version of Auspice for displaying each dataset.

You can run Augur and Auspice on your own computer and use them independently or together with your own builds, our core builds, or others’ group or community builds. You can even install Auspice on your own web server if you don’t want to host your datasets via nextstrain.org.

The Nextstrain CLI ties together all of the above to provide a consistent way to run pathogen workflows, access Nextstrain tools like Augur and Auspice across computing environments such as Docker, Conda, and AWS Batch, and publish datasets to nextstrain.org.

Nextclade is a web application and a command-line tool for performing viral genome alignment, mutation calling, clade assignment, quality checks, and phylogenetic placement. Nextclade can be used independently of other Nextstrain tools as well as integrated into workflows.

With this overview, you’ll be better prepared to install Nextstrain and run a workflow or contribute to development.