Independent evaluation of PlasmidCall in 432 carbapenem-resistant Enterobacterales isolates: analysis code
Year: 2026
Type: software
Abstract: This item holds the analysis code of the independent evaluation of PlasmidCall, a plasmid–chromosome classification model for short-read assembly contigs, in 432 carbapenem-resistant Enterobacterales isolates (NCBI BioProject PRJNA1133668). It accompanies the manuscript "PlasmidCall: a plasmid–chromosome classification model for genomic context assignment of antimicrobial resistance determinants with independent evaluation in carbapenem-resistant Enterobacterales".Contents. PlasmidCall_P114_analysis_code.zip holds the scripts that covered read retrieval and checking, depth capping, short-read assembly, the classifier panel and its parser, the fixed PlasmidCall predictions and their verification, the hybrid assemblies, the reference labels, the genomic (ANI) clusters, database exposure, scoring, the secondary endpoints, the main results table, paired comparisons 1–4, the sensitivity analysis and Figures 1–3. Every file is copied byte for byte from its source. FILES.tsv gives each file's size, SHA-256 and source, and whether it matches the digest recorded for it in the evaluation data; SHA256SUMS gives the SHA-256 of every other file in the zip. README.md, a copy of the one in the zip, gives the order of execution, the execution environment, what can be rerun and the known limitations.Related deposits. Evaluation data: doi:10.6084/m9.figshare.34021401. Native classifier outputs and execution records (Harvard Dataverse): doi:10.7910/DVN/Q5JNX9. PlasmidCall release v1.1.0, with the v1.2-General and v1.1 models: doi:10.6084/m9.figshare.34018380.v1; the four development models, with the code that applied them: doi:10.6084/m9.figshare.34018380.v2. The data of the earlier 150-genome evaluation: doi:10.5281/zenodo.22086357.Licence. MIT (LICENSE in the zip). File: PlasmidCall_P114_analysis_code.zip, SHA-256 905bebc52036d6487acb9c2ea61b26ac1f9fba37a060493fca6ef59417a38bdf.
Source: Figshare
Author: Vahhab Piranfar
Language: English
Subfield: Microbiology (medical)
Field: Medicine
Domain: Health Sciences
Open Access status: green
OpenAlex ID: W7219664772