Reference files for Cyclospora cayetanensis amplicon genotyping (CDC 8-marker panel): markers, PART windows, haplotype nomenclature and junction references

The four reference files needed to call haplotypes from Cyclospora cayetanensis amplicon sequencing with the CDC 8-marker panel, packaged as one citable unit with checksums and provenance.

These files are not new data. All four originate in CDC's published typing workflow, which places itself in the public domain. They are redeposited here unmodified so that an analysis can cite an immutable, versioned reference set by DOI instead of a repository path that may move, and so that a reader can verify by checksum that they used exactly the same references.

• markers.fa — the seven alignable amplicon reference sequences, with primers (7 records)
• parts.bed — the 24 PART windows, ~100 bp haplotype-calling intervals in coordinates relative to markers.fa
• haplotypes78.fa — the named haplotype nomenclature release used to name an exact-match call (78 records)
• junction.fa — the Mt-Junction reference windows, for the repeat-length locus that is not typed by alignment (20 records)

The first three are a matched set and must be used together. Column 4 of parts.bed keys the records in haplotypes78.fa, and parts.bed's coordinates only mean anything relative to markers.fa — a one-base difference in the marker reference silently shifts every PART window rather than raising an error.

Every file is byte-identical to its counterpart in CDC's repository, verified against the live repository at commit 5fbd865ddbbdba4b938a321a7c8f5b6e7f028bd2 (2022-08-05). markers.fa and parts.bed are unmodified single files; haplotypes78.fa and junction.fa concatenate upstream per-record FASTA files into one multi-FASTA each, with every sequence byte-identical to its upstream record. Per-file SHA-256 checksums and the full upstream path mapping are in the included README.md and SHA256SUMS.

CDC's repository states that it is in the public domain within the United States and that copyright and related rights worldwide are waived through CC0 1.0. This deposit is released under the same terms. CC0 imposes no attribution requirement, but please cite CDC's work as the source of the panel and the nomenclature; this deposit is a redistribution, not a contribution to the underlying data.