SCARPA: scaffolding reads with practical algorithms
Why this work is in the frame
A frame that forgets how it found something cannot be audited. These are the routes that admitted this work.
Bibliographic record
Abstract
MOTIVATION: Scaffolding is the process of ordering and orienting contigs produced during genome assembly. Accurate scaffolding is essential for finishing draft assemblies, as it facilitates the costly and laborious procedures needed to fill in the gaps between contigs. Conventional formulations of the scaffolding problem are intractable, and most scaffolding programs rely on heuristic or approximate solutions, with potentially exponential running time. RESULTS: We present SCARPA, a novel scaffolder, which combines fixed-parameter tractable and bounded algorithms with Linear Programming to produce near-optimal scaffolds. We test SCARPA on real datasets in addition to a simulated diploid genome and compare its performance with several state-of-the-art scaffolders. We show that SCARPA produces longer or similar length scaffolds that are highly accurate compared with other scaffolders. SCARPA is also capable of detecting misassembled contigs and reports them during scaffolding. AVAILABILITY: SCARPA is open source and available from http://compbio.cs.toronto.edu/scarpa.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
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 it