ReCycled: A Tool to Reset the Start of Circular Bacterial Chromosomes
Bibliographic record
Abstract
Abstract Summary (two sentences) For many publicly available bacterial genomes the chromosome start is not set at the replication initiation protein. This is a burden for comparative genomics studies as the synteny between such genomes cannot readily be assessed. Here, we present ReCycled, a tool for identifying and resetting the start of circular bacterial chromosomes. Availability and implementation Freely available on GitHub at https://github.com/Freevini/ReCycled under the GPL-3.0 license. Runs on all tested GNU/Linux systems. Contact Vincent Somerville, vincent@somerville.earth Supplementary Information The analyses, scripts and data to test the different pipelines are deposited online on zenodo (10.5281/zenodo.15170502).
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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 | 0.003 | 0.013 |
| Meta-epidemiology (narrow) | 0.003 | 0.002 |
| Meta-epidemiology (broad) | 0.002 | 0.002 |
| Bibliometrics | 0.003 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.003 | 0.003 |
| Open science | 0.003 | 0.005 |
| Research integrity | 0.002 | 0.003 |
| Insufficient payload (model declined to judge) | 0.097 | 0.055 |
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".