feat(qc): recombination: A: Weighted Threshold

.gitignore

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 /build/
 /data_dev*/
 /data_local*
-/data/
+/data/*
+!data/recomb/
 /docs/build/
 /e2e/cli/snapshots/
 /e2e/cli/tmp/

data/recomb/enpen/enterovirus/ev-d68/CHANGELOG.md

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+## 2025-12-10T13:21:04Z
+
+- Update alignment parameters in pathogen.json:
+    - Fix gap extension penalty
+    - Enable reverse-complement handling
+- Recompute tree topology (ML tree rerun)
+- Regenerate mutation labels for all clades
+- Update reference example sequences
+
+## 2025-11-20T19:02:04Z
+
+Add citation information to README.md
+
+## 2025-11-19T20:40:14Z
+
+Initial release of an Enterovirus D68 dataset for lineage classification!
+
+Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

data/recomb/enpen/enterovirus/ev-d68/README.md

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+# Enterovirus D68 dataset with reference Fermon
+
+| Key                  | Value                                                                 |
+|----------------------|-----------------------------------------------------------------------|
+| authors              | [Nadia Neuner-Jehle](https://eve-lab.org/people/nadia-neuner-jehle/), [Alejandra González-Sánchez](https://www.vallhebron.com/en/professionals/alejandra-gonzalez-sanchez), [Emma B. Hodcroft](https://eve-lab.org/people/emma-hodcroft/), [ENPEN](https://escv.eu/european-non-polio-enterovirus-network-enpen/)                                                 |
+| name                 | Enterovirus D68                                                       |
+| reference            | [AY426531.1](https://www.ncbi.nlm.nih.gov/nuccore/AY426531.1)         |
+| workflow             | https://github.com/enterovirus-phylo/nextclade_d68                    |
+| path                 | `enpen/enterovirus/ev-d68`                                            |
+| clade definitions    | A–C (D)                                                               |
+
+## Citation
+
+If you use this dataset in your research, please cite:
+
+> Neuner-Jehle, N., González Sánchez, A., Hodcroft, E. B., & European Non-Polio Enterovirus Network (ENPEN). (2025). *enterovirus-phylo/nextclade_d68: Enterovirus D68 Nextclade Dataset v1.0.0* (v1.0.0--2025-11-18). Zenodo. https://doi.org/10.5281/zenodo.17642338
+
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17642338.svg)](https://doi.org/10.5281/zenodo.17642338)
+
+## Scope of this dataset
+
+Based on full-genome sequences, this dataset uses the **Fermon reference sequence** ([AY426531.1](https://www.ncbi.nlm.nih.gov/nuccore/AY426531.1)), originally isolated in 1962. It serves as the basis for quality control, clade assignment, and mutation calling across global EV-D68 diversity.
+
+*Note: The Fermon reference differs substantially from currently circulating strains.* This is common for enterovirus datasets, in contrast to some other virus datasets (e.g., seasonal influenza), where the reference is updated more frequently to reflect recent lineages.
+
+To address this, the dataset is *rooted* on a Static Inferred Ancestor — a phylogenetically reconstructed ancestral sequence near the tree root. This provides a stable reference point that can be used, optionally, as an alternative for mutation calling.
+
+## Features
+
+This dataset supports:
+
+- Assignment of subgenotypes
+- Phylogenetic placement
+- Sequence quality control (QC)
+
+## Subgenogroups of Enterovirus D68
+
+Clade designations follow the global diversity of EV-D68: A (A1–A2/D), B (B1–B3), and C. The label "pre-ABC" indicates old, basal lineages that are no longer circulating. Sequences labeled "pre-ABC" or "unassigned" may indicate sequencing or assembly issues and should be assessed carefully.
+
+These designations are based on the phylogenetic structure and mutations, and are widely used in molecular epidemiology, similar to subgenotype systems for other enteroviruses. Unlike influenza (H1N1, H3N2) or SARS-CoV-2, there is no universal, standardized global lineage nomenclature for enteroviruses. Naming follows conventions from published studies and surveillance practices.
+
+## Reference types
+
+This dataset includes several reference points used in analyses:
+- *Reference:* RefSeq or similarly established reference sequence. Here Fermon.
+
+- *Parent:* The nearest ancestral node of a sample in the tree, used to infer branch-specific mutations.
+
+- *Clade founder:* The inferred ancestral node defining a clade (e.g., A2, B3). Mutations "since clade founder" describe changes that define that clade.
+
+- *Static Inferred Ancestor:* Reconstructed ancestral sequence inferred with an outgroup, representing the likely founder of EV-D68. Serves as a stable reference.
+
+- *Tree root:* Corresponds to the root of the tree, it may change in future updates as more data become available.
+
+All references use the coordinate system of the Fermon sequence.
+
+## Issues & Contact
+- For questions or suggestions, please [open an issue](https://github.com/enterovirus-phylo/nextclade_d68/issues) or email: eve-group[at]swisstph.ch
+
+## What is a Nextclade dataset?
+
+A Nextclade dataset includes the reference sequence, genome annotations, tree, clade definitions, and QC rules. Learn more in the [Nextclade documentation](https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html).

data/recomb/enpen/enterovirus/ev-d68/genome_annotation.gff3

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+##gff-version 3
+#!gff-spec-version 1.21
+#!processor NCBI annotwriter
+##sequence-region AY426531.2 1 7367
+##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=42789
+# seqname	source	feature	start	end	score	strand	frame	attribute
+AY426531.1	Genbank	region	1	7367	.	+	.	ID=AY426531.1:1..7367;Dbxref=taxon:42789;country=USA;gb-acronym=EV-D68;gbkey=Src;mol_type=genomic RNA;note=prototype strain of Enterovirus 68;old-name=Enterovirus 68;strain=Fermon
+AY426531.1	Genbank	CDS	733	939	.	+	.	Name=VP4;gbkey=Prot;product=VP4;ID=id-AAR98503.1:1..69
+AY426531.1	Genbank	CDS	940	1683	.	+	.	Name=VP2;gbkey=Prot;product=VP2;ID=id-AAR98503.1:70..317
+AY426531.1	Genbank	CDS	1684	2388	.	+	.	Name=VP3;gbkey=Prot;product=VP3;ID=id-AAR98503.1:318..552
+AY426531.1	Genbank	CDS	2389	3315	.	+	.	Name=VP1;gbkey=Prot;product=VP1;ID=id-AAR98503.1:553..861
+AY426531.1	Genbank	CDS	3316	3756	.	+	.	Name=2A;gbkey=Prot;product=2A;ID=id-AAR98503.1:862..1008
+AY426531.1	Genbank	CDS	3757	4053	.	+	.	Name=2B;gbkey=Prot;product=2B;ID=id-AAR98503.1:1009..1107
+AY426531.1	Genbank	CDS	4054	5043	.	+	.	Name=2C;gbkey=Prot;product=2C;ID=id-AAR98503.1:1108..1437
+AY426531.1	Genbank	CDS	5044	5310	.	+	.	Name=3A;gbkey=Prot;product=3A;ID=id-AAR98503.1:1438..1526
+AY426531.1	Genbank	CDS	5311	5376	.	+	.	Name=3B;gbkey=Prot;product=3B;ID=id-AAR98503.1:1527..1548
+AY426531.1	Genbank	CDS	5377	5925	.	+	.	Name=3C;gbkey=Prot;product=3C;ID=id-AAR98503.1:1549..1731
+AY426531.1	Genbank	CDS	5926	7296	.	+	.	Name=3D;gbkey=Prot;product=3D;ID=id-AAR98503.1:1732..2188