-
Notifications
You must be signed in to change notification settings - Fork 0
Datasets
Three dataset tiers, each testing a different aspect of profiler behavior. Manifests live in data/datasets_*.txt (one fastq path per line) and are passed to the profiler driver via --dataset-list.
| Tier | Tests | Ground truth | Manifest |
|---|---|---|---|
| Simulated | algorithm under known composition | exact (simulated) | data/datasets_simulated.txt |
| Mock (D6331) | real sequencing of a defined community | manufacturer composition |
data/datasets_mock_pacbio.txt, data/datasets_mock_ont.txt
|
| Clinical (DYN) | real-world inter-method concordance | none (Illumina baseline as proxy) | cohort cache (dyn_load_all.py) |
PacBio and ONT reads simulated from a gut profile fitted with MIMIC and generated by PBSIM3 (data/simulated/{pacbio,ont}/sim_*.fastq); truth is the PBSIM3 reference taxon list. Used by Fig 2.
The simulated fastqs and their per-species truth tables (sim_{pacbio,ont}_truth_abundance.tsv) are hosted on Zenodo, record 20496925.
Both platforms are simulated from the same composition, so at simulated coverage sketch tools recover identical taxa regardless of platform error model - this tier tests algorithmic capability, not ONT-vs-PacBio error transfer.
A defined community on both platforms; truth is the manufacturer composition. Used by Fig 3 (detection), Fig 4 (operating characteristic across the threshold sweep), and Figs 5-6 (abundance + concordance); supplementary panels in Figs S2-S5.
PacBio HiFi (data/datasets_mock_pacbio.txt) - shared Shoreline Breaker extraction, differing input mass:
- SRR13128013 - low input
- SRR13128014 - standard input
ONT (data/datasets_mock_ont.txt) - two libraries differing only in DNA-extraction chemistry: D6331_Zymo (Zymo Quick-DNA) and D6331_Qiagen (Qiagen PowerSoil Pro), from the ZymoBIOMICS data portal.
Antibiotic-perturbed gut metagenomes on PacBio + ONT with matched Illumina baselines. No defined truth, so the analysis reports cross-tool / cross-platform agreement. Used by Fig 7 (heatmaps) and Fig 8 (alpha-diversity); ONT-cohort supplementary panels in Figs S6-S8. Cohort cache built by scripts/analysis/dyn_load_all.py.
- Data Fetch - download the reads + references
- Reproduction - which dataset feeds which figure