Glossary

Glossary

What is this?

Short definitions of every term this wiki uses.

Why does it matter?

Half of learning a pipeline is learning its words.

What do I do?

Look a term up when a page uses it.

flowchart LR
    S["Snakemake<br/>(runs everything)"] --> N["Nextclade<br/>(clades + QC)"]
    S --> A["Augur<br/>(filter, tree, export)"]
    A --> J["Auspice JSON"]
    J --> V["Auspice<br/>(viewer, nextstrain.org)"]

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How the main tools fit together.

Term	Meaning
Augur	Nextstrain's command-line toolkit for filtering, aligning, building and dating trees, and exporting them (augur filter, augur tree, ...).
Auspice	The viewer that shows the trees, on nextstrain.org or locally (auspice view).
Auspice JSON	The file Auspice reads: one per build, in auspice/, plus a _tip-frequencies.json sidecar.
Build	One tree with its metadata, e.g. H3N2 HA. This pipeline makes 24 segment builds and 3 whole-genome builds.
Clade / subclade	Named branches of the tree, assigned by Nextclade from the HA segment. Subclade is the current name (e.g. J.2, K, D.3.1.1, C.5.6). Clade in our trees is Nextclade's legacy-clade (e.g. 3C.2a1b.2a.2a.3a.1, 6B.1A.5a.2a.1, V1A.3a.2): Nextclade's own clade column now repeats the subclade.
Clock filter	Removing tips that sit too far from the molecular-clock expectation (--clock-filter-iqd).
Conda environment	A self-contained set of tools and their exact versions. This pipeline uses one called pekosz-nextstrain, built by bash scripts/build_env.sh and switched on with conda activate pekosz-nextstrain.
Config	Settings files in config/ (references, colors, report options, tutorial/production switches) that change what the pipeline does without changing code.
Control	A no-template or water sample (NTC, water...) run alongside specimens; never a patient sample.
Coverage	Fraction of the reference a sequence covers (Nextclade); builds keep ≥ 0.9.
DAG	Directed acyclic graph: the map of which steps depend on which. Snakemake builds it from file names; rulegraph.png draws it.
Dry run	snakemake -n: shows what would run, runs nothing.
EPI_ISL / EPI_SET	A GISAID isolate accession / a citable GISAID identifier for a set of sequences.
fludb	The small SQLite database (fludb.db) the pipeline builds to sort sequences into builds.
flusort	The lab's BLAST-based tool that types each segment (A/B, H and N subtype).
GISAID	The database where flu sequences are shared under a licence that forbids redistribution.
Hook	A check git runs automatically before a commit or a push (.githooks/).
JHH	Johns Hopkins Hospital network; source of the clinical sequences (Mostafa Lab).
Metadata	The table describing each specimen (ID, run, date, passage).
Nextclade	Tool that aligns sequences, assigns clades and scores quality.
Nextstrain Docker runtime	Nextstrain's prepackaged container (nextstrain shell). Used by older versions of this pipeline; no longer supported here (why).
Nextstrain	The open-source project (and website) for real-time pathogen tracking that Augur and Auspice belong to.
Passage history	How a virus was grown before sequencing (vtm = sequenced directly from viral transport medium; E3 = three passages in eggs).
Profile	A saved set of Snakemake options (profiles/default/).
QC status	Nextclade's overall quality call: good, mediocre or bad. Builds keep good and mediocre.
Rule	One step in Snakemake (inputs, outputs, command).
Run ID	A run's start time, YYYYMMDDTHHMMSS, prefixing every file in .run/.
Segment	One of the 8 RNA pieces of the flu genome: PB2, PB1, PA, HA, NP, NA, MP, NS.
Sequencing run	One batch on the sequencer, named like IV26Run8.
Snakemake	The workflow tool that runs the pipeline's steps in the right order.
Snapshot	A dated archive of a whole run (snapshots/*.tar.gz).
Tier	How risky a change is, 0 to 3 (Best Practices).
Wildcard	A placeholder in a Snakemake file path, like {subtype} or {segment}, filled in for each build.

Troubleshooting / FAQ

• A term is missing. Add it here in the same PR that introduces it (Coding with Agents).

Next step → Roadmap & Known Issues