Full-length cox1 barcoding of Dibothriocephalus spp. from Nanopore tiling amplicons: analysis pipeline and run reports

Résumé fourni par la source

Reproducible analysis pipeline accompanying the article "Molecular Identification of Zoonotic Dibothriocephalus Tapeworms in Introduced Salmonids from Chilean Patagonia Using Low-Cost Nanopore Sequencing of the Full cox1 Barcode". The pipeline assembles the near-complete mitochondrial cox1 gene of Dibothriocephalus latus and D. dendriticus from three overlapping PCR amplicons sequenced on an Oxford Nanopore Flongle R10.4.1 flow cell. Each specimen is mapped independently against two species references and assembled against the better-fitting one; reads are assigned to a single amplicon each, so per-amplicon counts sum to the mapped total; assemblies are trimmed to the interval covered by the tiling design; and a per-amplicon concordance check flags specimens whose amplicons disagree on species assignment. The archive contains the pipeline script, the amplicon coordinate and primer table, the conda environment specification, a helper for retrieving the reference sequences from GenBank, the full documentation, the tab-separated reports produced by the run described in the article, and the 24 assembled barcodes in FASTA format. No reference sequence is bundled by design: both references must be downloaded by accession so that the exact sequences used remain traceable. Raw sequencing reads are deposited separately in the NCBI Sequence Read Archive.

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