Additional file 3 of De novo assembly of the olive fruit fly (Bactrocera oleae) genome with linked-reads and long-read technologies minimizes gaps and provides exceptional Y chromosome assembly
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
Additional file 3: Figure S1. Schematic of the method used to generate the main assembly reported. Figure S2. Genome size and heterozygosity estimation. Figure S3. Contig length at different Nx values for assemblies in Supplementary Table S3. Figure S4. Contiguity plot generated using Quast. Figure S5. Contig length at different Nx values for assemblies in Supplementary Table S4. Figure S6. Plot showing Y chromosome scaffolds/contigs identified in 3 different assemblies (Supplementary Table S4). Figure S7. Total length of scaffolds that were localized to each polytene chromosome and XY chromosomes. Figure S8. Alignment rates of RNA-seq reads from 12 different Bactrocera oleae datasets (see Supplementary Table S9). Figure S9. Complete Basic Universal Single Copy Orthologs (BUSCOs) identified in genome assemblies (Supplementary Table S3). Figure S10. Schematic of the PiRATE pipeline. Figure S11. Histogram of transcripts read lengths. Figure S12. Percentage of Arthropoda Basic Universal Single Copy Orthologs (BUSCOs) captured in 19 arthropod transcriptomes. Figure S13. Number of JAMg predicted B. oleae genes located on the scaffolds assigned to polytene element. Figure S14. Gene ontology (GO) classification of B. oleae JAMg predicted proteins. Figure S15. Detailed orthogroup distribution. Figure S16. Hierarchical clustering of 1100 most variable genes among the 4 metamorphotic stages. Figure S17. Most significantly enriched gene ontology (GO) terms among genes that only peak during development. Figure S18. Contig length at different Nx values for assemblies of selected insects.
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) | 0.334 | 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