================
Parts of a whole
================

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

.. graphviz::
    :align: center

    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;
    }

:term:`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.

.. graphviz::
    :align: center

    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=""];
    }

:term:`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
<https://nextstrain.org/mumps/na>`__.

.. figure:: /images/mumps.png

    Auspice displaying Mumps genomes from North America.

:term:`Datasets<phylogenetic dataset>` are produced by Augur and
visualized by Auspice.  These files are often referred to as :term:`JSONs`
colloquially because they use a generic data format called JSON.

.. graphviz::
    :align: center

    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;
    }

A :term:`build` is a recipe of several commands and data that produce a single :term:`dataset`.

.. graphviz::
    :align: center

    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;
    }

A :term:`workflow` can bundle one or more related :term:`builds<build>` and are often automated by workflow managers
such as `Snakemake <https://snakemake.readthedocs.io>`__, `Nextflow <https://nextflow.io>`__
and `WDL <https://openwdl.org>`__.

Our :term:`pathogen repositories<pathogen repository>` are organized as `Git repositories <https://git-scm.com>`__
hosted on `GitHub <https://github.com/nextstrain>`__. Each repository can contain
one or more workflows.

.. graphviz::
    :align: center

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        graph [
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            fontsize=12,
        ];
        node [
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            style="rounded, filled",
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            fontsize=12,
            height=0.1,
            colorscheme=paired10,
            pad=0.1,
            margin=0.1,
        ];
        rankdir=LR;

        subgraph cluster_ncov {
            label = "SARS-CoV-2 repository";
            subgraph cluster_ncov_phylo {
                label = "Phylogenetic workflow";
                build0 [width=1, label="Global build"];
                build1 [width=1, label="Africa build"];
                build2 [width=1, label="Europe build"];
                output0 [width=1, label="dataset"];
                output1 [width=1, label="dataset"];
                output2 [width=1, label="dataset"];
                ellipses1 [width=1, label="...", penwidth=0, fillcolor="white"];
                ellipses2 [width=1, label="...", penwidth=0, fillcolor="white"];
            }
        }

        subgraph cluster_zika {
            label = "Zika repository";
            nojustify = true;
            subgraph cluster_zika_ingest {
                label = "Ingest workflow";
                build3 [width=1, label="ingest build"];
                output3 [width=1, label="ingest dataset"];
            }
            subgraph cluster_zika_phylo {
                label = "Phylogenetic workflow";
                build4 [width=1, label="phylogenetic build"];
                output4 [width=1, label="dataset"];
            }
        }

        subgraph cluster_mpox {
            label = "Mpox repository";
            subgraph cluster_mpox_ingest {
                label = "Ingest workflow";
                build5 [width=1, label="ingest build"];
                output5 [width=1, label="ingest dataset"];
            }
            subgraph cluster_mpox_phylo {
                label = "Phylogenetic workflow";
                build6 [width=1, label="mpxv build"];
                build7 [width=1, label="hmpxv1 build"];
                build8 [width=1, label="hmpxv1_big build"];
                output6 [width=1, label="dataset"];
                output7 [width=1, label="dataset"];
                output8 [width=1, label="dataset"];

            }
            subgraph cluster_mpox_nextclade {
                label = "Nextclade workflow";
                build9 [width=1, label="all-clades build"];
                build10 [width=1, label="clade-iib build"];
                build11 [width=1, label="lineage-b.1 build"];
                output9 [width=1, label="Nextclade dataset"];
                output10 [width=1, label="Nextclade dataset"];
                output11 [width=1, label="Nextclade dataset"];

            }
        }

        build0 -> output0;
        build1 -> output1;
        build2 -> output2;
        build3 -> output3;
        build4 -> output4;
        build5 -> output5;
        build6 -> output6;
        build7 -> output7;
        build8 -> output8;
        build9 -> output9;
        build10 -> output10;
        build11 -> output11;

        {
            edge[style=invis];
            output0 -> build3; // arrange clusters on same row
            output3 -> build5; // arrange clusters on same row
            ellipses1 -> ellipses2;
        }
    }

`nextstrain.org <https://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 :doc:`Nextstrain Groups </guides/share/groups/index>`
and :doc:`community pages </guides/share/community-builds>` which are
maintained and :doc:`shared </guides/share/index>` by many other people.  The
website incorporates a customized version of Auspice for displaying each
dataset.

You can run :term:`Augur` and :term:`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 :doc:`your own web server <auspice:server/overview>` if you don't want
to host your datasets via nextstrain.org.

The :term:`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.

:doc:`Nextclade <nextclade:index>` 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 :doc:`install Nextstrain
</install>` and :doc:`run a workflow </tutorials/running-a-phylogenetic-workflow>` or :doc:`contribute
to development </guides/contribute/index>`.