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N. gonorrhoeae Euro-GASP Genotype Data Use Case 1

Source: R/data.R
eurogasp_geno_raw.Rd

Raw concatenated output from AMRFinderPlus v4.0.23 (database 2025-03-25.1) run on Neisseria gonorrhoeae genome assemblies from three Euro-GASP genomic surveys (2013, 2018, 2020). Assemblies were generated with SPAdes v3.15.5 and quality-assessed with QUAST v5.1. This object serves as the genotype input for import_amrfp.

Usage

eurogasp_geno_raw

Format

eurogasp_geno_raw A data frame with 54,764 rows and 24 columns:

  • Name: Sample identifier (ENA run accession).

  • Protein identifier: Protein identifier (not used for N. gonorrhoeae assemblies; all NA).

  • Contig id: Assembly contig identifier.

  • Start, Stop: Start and stop positions of the AMR element on the contig.

  • Strand: Strand orientation (+ or -).

  • Element symbol: AMRFinderPlus element symbol (gene name and/or mutation, e.g. gyrA_S91F).

  • Sequence name: Full descriptive name of the AMR element.

  • Scope: AMRFinderPlus scope (core or plus).

  • Element type: Type of AMR element (e.g. AMR).

  • Element subtype: Subtype of AMR element (e.g. POINT, AMR).

  • Class: Antibiotic class (e.g. QUINOLONE, BETA-LACTAM).

  • Subclass: Antibiotic subclass (e.g. CEPHALOSPORIN, TETRACYCLINE).

  • Method: Detection method used by AMRFinderPlus (e.g. POINTX, BLASTX).

  • Target length, Reference sequence length, Alignment length: Sequence length metrics (bp).

  • % Coverage of reference sequence: Percentage of reference sequence covered by the alignment.

  • % Identity to reference sequence: Percentage identity to the closest reference sequence.

  • Accession of closest sequence: NCBI accession of the closest reference sequence.

  • Name of closest sequence: Name of the closest reference sequence.

  • HMM id, HMM description: HMM-based annotation fields (all NA for this dataset).

  • Hierarchy node: Gene hierarchy node name, required for import_amrfp (enabled by --print_node flag).

Source

ENA projects PRJEB9227, PRJEB34068, PRJEB58139. See also Harris et al. (2018) https://doi.org/10.1016/S1473-3099(18)30225-1, Sánchez-Busó et al. (2022) https://doi.org/10.1016/S2666-5247(22)00044-1, and Golparian et al. (2024) https://doi.org/10.1016/S2666-5247(23)00370-1.