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A software tool 'CroCo' detects pervasive cross-species contamination in next generation sequencing data
Paul Simion1,2, Khalid Belkhir1, Clémentine François1
1Institut des Sciences de l'Evolution (ISEM), UMR 5554, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France.
BMC Biology
|March 7, 2018
Summary
Cross contamination in RNA sequencing is a significant problem that can skew results. The new CroCo software efficiently identifies and removes these contaminants from assembled transcriptomes, ensuring more accurate downstream analyses.
Area of Science:
- Bioinformatics
- Genomics
- Molecular Biology
Background:
- Multiplex sequencing often involves processing multiple RNA samples together.
- While sample barcodes separate known samples, cross-contamination between different species processed in parallel poses a risk.
- Such cross-contamination can severely impact downstream biological analyses.
Purpose of the Study:
- To develop a computational tool for identifying and removing cross-contaminants from assembled transcriptomes.
- To assess the prevalence and impact of cross-contamination in real-world sequencing datasets.
- To provide a reliable method for ensuring data integrity in comparative transcriptomic studies.
Main Methods:
- Development of CroCo, a software package for cross-contaminant detection and removal.
- Testing CroCo using multiple published sequence datasets, including real and simulated data.
- Evaluation of the impact of cross-contamination on molecular phylogenetic analyses.
Main Results:
- Cross-contamination is consistently present in real sequencing datasets at varying levels.
- CroCo effectively detects and removes cross-contaminants with high accuracy in both real and simulated data.
- Unremoved contaminants can significantly and detrimentally affect downstream comparative analyses, such as phylogenetics.
Conclusions:
- Cross-contamination is a pervasive issue in transcriptomic datasets that can lead to erroneous conclusions.
- CroCo is a user-friendly, database-independent tool for accurately identifying and removing cross-contaminants.
- Implementing CroCo as a standard cleaning step is recommended for multi-sample transcriptome sequencing workflows.