Plasmid Profiler: Comparative Analysis of Plasmid Content in WGS Data
Bibliographic record
Abstract
Abstract Summary Comparative analysis of bacterial plasmids from whole genome sequence (WGS) data generated from short read sequencing is challenging. This is due to the difficulty in identifying contigs harbouring plasmid sequence data, and further difficulty in assembling such contigs into a full plasmid. As such, few software programs and bioinformatics pipelines exist to perform comprehensive comparative analyses of plasmids within and amongst sequenced isolates. To address this gap, we have developed Plasmid Profiler, a pipeline to perform comparative plasmid content analysis without the need for de novo assembly. The pipeline is designed to rapidly identify plasmid sequences by mapping reads to a plasmid reference sequence database. Predicted plasmid sequences are then annotated with their incompatibility group, if known. The pipeline allows users to query plasmids for genes or regions of interest and visualize results as an interactive heat map. Availability and Implementation Plasmid Profiler is freely available software released under the Apache 2.0 open source software license. A stand-alone version of the entire Plasmid Profiler pipeline is available as a Docker container at https://hub.docker.com/r/phacnml/plasmidprofiler_0_1_6/ . The conda recipe for the Plasmid R package is available at: https://anaconda.org/bioconda/r-plasmidprofiler The custom Plasmid Profiler R package is also available as a CRAN package at https://cran.r-project.org/web/packages/Plasmidprofiler/index.html Galaxy tools associated with the pipeline are available as a Galaxy tool suite at https://toolshed.g2.bx.psu.edu/repository?repository_id=55e082200d16a504 The source code is available at: https://github.com/phac-nml/plasmidprofiler The Galaxy implementation is available at: https://github.com/phac-nml/plasmidprofiler-galaxy Contact Email: gary.vandomselaar@canada.ca Address: National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, Canada Supplementary information Documentation: http://plasmid-profiler.readthedocs.io/en/latest/
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.005 | 0.007 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.002 |
| Bibliometrics | 0.004 | 0.004 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.002 | 0.001 |
| Open science | 0.001 | 0.002 |
| Research integrity | 0.001 | 0.002 |
| Insufficient payload (model declined to judge) | 0.017 | 0.011 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".