Split by dengue serotype (denv1-denv4)

Description

Implement strategies (or an ensemble of strategies for cross-validation) to produce pairs of sequences_{serotype}.fasta and metadata_{serotype}.tsv files.

Context

Following the merge of https://github.com/nextstrain/dengue/pull/13, all ingested dengue records now exist in a unified pair of sequences.fasta and metadata.tsv files.

For subsequent analysis https://github.com/nextstrain/dengue/pull/18, and to maintain consistency with the previous approach and ensure a seamless integration with the phylogenetic pipeline, it is necessary to separate these files based on dengue serotypes (e.g., from sequences_denv1.fasta to sequences_denv4.fasta).

Possible solution(s)

Rely on NCBI taxon id annotations for serotype segregation

Historically, for dengue, we obtained each serotype individually in this code, leading to redundant fetching and processing of each sequence. Now that we're using ncbi datasets, these numeric IDs are recorded in a virus-tax-id field, that we can use to separate the serotypes.

Notably, this method carries the risk of missing sequences in individual serotype builds if NCBI did not annotate the record with the lineage ID. (~3k records) which can potentially be further refined with a nextclade all dataset.

Create a Nextclade dataset for finer subtype classification

Originally, the plan was to leverage Nextclade assignment to categorize records into major dengue serotypes and subsequent minor subtypes https://github.com/nextstrain/dengue/pull/16. However, due to the diversity within dengue, the major serotype classification did not align with expectations. Therefore the idea is to rely on NCBI taxon ids for major serotypes, and nextclade datasets for within-serotype sub-classification.

An ensemble method

Ideally, employ a combination of the above methods to consistently and accurately classify records into major serotypes and minor subtypes.

Tasks to solve this issue

[x] https://github.com/nextstrain/dengue/pull/20
[x] https://github.com/nextstrain/dengue/pull/16
- [ ] which possibly requires https://github.com/nextstrain/dengue/pull/25

nextstrain / dengue