2026-10-09T10:29:19Z https://api.figshare.com/v2/oai

oai:figshare.com:article/34018380 2026-10-04T01:09:08Z category_24184 category_24361 item_type_9 month_year_10_2026

PlasmidCall: code and frozen models for plasmid-origin classification of short-read contigs Vahhab Piranfar (24705250) Bioinformatic methods development Microbial genetics PlasmidCall plasmid plasmid-origin classification contig classification short-read assembly antimicrobial resistance bacterial genomics <p dir="ltr">Code and frozen models of PlasmidCall, which classifies short-read assembly contigs as plasmid- or chromosome-derived from the calls of twelve published plasmid classifiers. This item archives release v1.1.0 of https://github.com/piranfar/PlasmidCall (git tag v1.1.0, commit 19e840546799a9d404fdf77c0a099df206efab2f) as one zip file.</p><p dir="ltr">The release contains the frozen PlasmidCall v1.2-General model (a logistic regression on the twelve classifiers' categorical calls, provided as a portable JSON file that needs only numpy and as a scikit-learn pickle) and PlasmidCall v1.1 (histogram gradient boosting, a scikit-learn 1.9.0 pickle), with their SHA-256 digests; the frozen panel-output parser; a standalone scorer; tests showing that the scorer reproduces the frozen outputs of the 150-isolate evaluation exactly (the default run checks a 200-row fixture; the full 19,320-contig check runs when given the P1.13 table from the data deposit); and the design records, evidence receipts and derived tables of that evaluation.</p><p dir="ltr">The bulk data of the evaluation (parsed classifier calls, assemblies, execution receipts and the joined truth table) are in a separate data deposit, doi:10.5281/zenodo.22086357 (version 1.0.0; the concept DOI 10.5281/zenodo.22086356 resolves to the latest version). That deposit holds no model files; its Part 1 holds as-executed copies of the P1.13 run scripts, including the frozen parser, under CC BY 4.0. No third-party program or database is redistributed.</p><p dir="ltr">Licences: every .py, .sh and .diff file and the model files under models/ other than Markdown are under MIT (LICENSE); everything else, including documentation, tables, fixtures and metadata, is under CC BY 4.0 (LICENSE-DATA). Figshare records one licence per item, so MIT is shown on this page; the LICENSE and LICENSE-DATA files in the zip set the licence of each file.</p><p dir="ltr">File: PlasmidCall-1.1.0.zip, SHA-256 a2218569122588e1df596a93ac3294cce788f2a52aa7cd7a77ea32627614fc56. CHECKSUMS.sha256 inside the zip gives the SHA-256 of every released file.</p><p><b>This version adds four development models.</b> PlasmidCall_P114_ladder_models.zip holds the four development models of PlasmidCall (A, B_nb, C and C_sc_nb_iso) used in the independent evaluation of PlasmidCall in 432 carbapenem-resistant Enterobacterales isolates (BioProject PRJNA1133668), and the code that applied them. The four models differ only in their input blocks (prespecified ablation ladder). The models and their decision thresholds were fixed in amendments 2 and 3 of the time-stamped analysis plan on 2026-09-21, before any read of that cohort was retrieved. The zip is complementary to PlasmidCall release v1.1.0 (PlasmidCall-1.1.0.zip, published as version 1 of this item, doi:10.6084/m9.figshare.34018380.v1), which holds the released classifier, PlasmidCall v1.2-General, with PlasmidCall v1.1 and the router; the development models are not part of that release. The README in the zip gives each model's inputs, threshold and file SHA-256, the training set and the limitations. Every file in PlasmidCall_P114_ladder_models.zip is under the MIT licence (its LICENSE file). The data of the independent evaluation, including each model's fixed scores, are at doi:10.6084/m9.figshare.34021401, and the analysis code of the evaluation at doi:10.6084/m9.figshare.34063578. File: PlasmidCall_P114_ladder_models.zip, SHA-256 eb57815585085b0477d9068f23039ff9e6f0bf83ccf2366110f73394d389c90d.</p> 2026-10-04T01:09:08Z Software Software 10.6084/m9.figshare.34018380.v2 https://figshare.com/articles/software/PlasmidCall_code_and_frozen_models_for_plasmid-origin_classification_of_short-read_contigs/34018380 MIT