CroCoDeEL paper - Supplementary Data

Supplementary materials for: Goulet, L. et al. "CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomic data" bioRxiv (2025). https://doi.org/10.1101/2025.01.15.633153 📁 Newly Sequenced Samples Uncontaminated and intentionally contaminated samples used to illustrate the concept of the contamination line: PRJEB83730.meteor.tab — Meteor species abundance profiles PRJEB83730.conta_cases_scatterplots.pdf — Scatterplots of contamination cases 📁 Training Dataset Semi-simulated dataset used to train the Random Forest model: training_dataset.metadata.tab — Metadata describing the dataset training_dataset.meteor.tsv.xz — Meteor species abundance profiles, with species shuffled within pairs 📁 Real Test Datasets Real datasets used to assess CroCoDeEL's classification performance compared to human experts: PRJEB12449.meteor.tab — Real test dataset 1 (Meteor species abundance profiles) PRJEB12449.conta_cases_scatterplots.pdf — Scatterplots of contamination cases PRJEB10878.meteor.tab — Real test dataset 2 (Meteor species abundance profiles) PRJEB10878.conta_cases_scatterplots.pdf — Scatterplots of contamination cases PRJEB6337.meteor.tab — Real test dataset 3 (Meteor species abundance profiles) PRJEB6337.conta_cases_scatterplots.pdf — Scatterplots of contamination cases 📁 Other Benchmark Dataset Semi-simulated test dataset used to assess the impact of sequencing depth, contamination rates, and taxonomic profilers on CroCoDeEL’s performance: PRJNA763023_PRJDB4176.meteor.tab — Meteor species abundance profiles PRJNA763023_PRJDB4176.metaphlan4.tab — MetaPhlAn4 species abundance profiles PRJNA763023_PRJDB4176.sylph_gtdb_r214.tab — Sylph species profiles (GTDB r214) PRJNA763023_PRJDB4176.metaphlan4_filtered.tab — Filtered MetaPhlAn4 abundance profiles 📁 Lou et al. Dataset (Plates 2 & 3) PRJNA698986_P2.meteor.tab — Plate 2: Meteor species abundance profiles PRJNA698986_P2.conta_cases_scatterplots.pdf — Contamination cases (Plate 2) PRJNA698986_P3.meteor.tab — Plate 3: Meteor species abundance profiles PRJNA698986_P3.conta_cases_scatterplots.pdf — Contamination cases (Plate 3) 📁 PRJNA352475 (Ferretti et al.) PRJNA352475.meteor.tab — Meteor species abundance profiles PRJNA352475.conta_cases_scatterplots.pdf — Scatterplots of contamination cases detected by CroCoDeEL 📁 PRJEB32731 (TwinsUK) PRJEB32731.meteor.tab — Meteor species abundance profiles PRJEB32731.conta_cases_scatterplots.pdf — Scatterplots of contamination cases detected by CroCoDeEL