Additional file 2 of Identification of plasmids in avian-associated Escherichia coli using nanopore and illumina sequencing
Bibliographic record
Abstract
Additional file 2: Figure S1. Quality control parameters determined for different types of hybrid genome assembly. Strip plots show parameter values for N50 (A), number of contigs (B), largest contig (C), total length (D) and GC content (E), for hybrid WGS assemblies from 19 E. coli isolates, as determined by Quast. Bars represent the mean parameter values corresponding to each type of hybrid assembly: 1) HLF, Illumina + Nanopore Ligation + filtered; 2) HLUF, Illumina + Nanopore Ligation + unfiltered; 3) HRF, Illumina + Nanopore Rapid + filtered; and 4) HRUF, Illumina + Nanopore Rapid + unfiltered. There were no significant differences in quality parameters between each assembly type as determined by t-test (P > 0.05). Figure S2. Quality control parameters determined for different types of long-read genome assembly.Box and whisker plots show parameter values for N50 (A), number of contigs (B), largest contig (C), total length (D) and GC content (E), for long read WGS assemblies from 19 E. coli isolates, as determined by Quast. The line in each box represents the mean parameter value corresponding to each type of long-read (L) assembly: 1) LLF, Nanopore Ligation+ filtered; 2) LLUF, Nanopore Ligation + unfiltered; 3) LRF, Nanopore Rapid + filtered; and 4) LRUF, Nanopore Rapid + unfiltered. Statistical significance in any pairwise comparison was determined using ttests (P < 0.05, *; P < 0.01,**). All other pairwise comparisons were not significant (P > 0.05). Figure S3. The effect of polishing long read sequence assemblies on plasmid detection by MOB-suite.The total numbers of detected plasmids are shown for long-read DNA sequence assemblies (Nanopore Ligation or Rapid kits, filtered or unfiltered) prepared from 19 E. coli isolates. The assemblies were either unpolished, polished with raw Nanopore reads, or the long-read assemblies were polished with Illumina reads to generate a hybrid assembly, prior to analysis by MOB-suite software. The values were compared between groups using t-tests and determined not to be significantly different (P > 0.05, ns). Table S1. DNA sequencing parameters for plasmid extraction kit samples prepared from two avian-associated E. coli isolates.
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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 | 0.002 | 0.020 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.002 | 0.004 |
| Science and technology studies | 0.002 | 0.000 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.003 | 0.002 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.838 | 0.222 |
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".