CroCo

CroCo identifies and removes cross-contamination in high-throughput sequencing (HTS) assembled transcriptomes to preserve the accuracy of downstream comparative and molecular phylogenetic analyses.

Key Features:

• Cross-contamination detection: Analyzes assembled transcriptomes to detect sequences that may have originated from unintended species.
• Contaminant removal: Eliminates detected contaminant sequences from transcriptome assemblies to retain authentic RNA-derived sequences for analysis.
• Multiplexing-aware analysis: Targets contaminations arising from sample mixing during multiplexed sequencing that are not resolved by sample barcodes alone.
• Validation on datasets: Demonstrated efficacy using both real and simulated datasets, reporting high accuracy and efficiency.
• Database-independent operation: Performs detection and cleaning without relying on external sequence databases.

Scientific Applications:

• Molecular phylogenetics: Removes cross-species contaminants that can mislead phylogenetic inference and downstream evolutionary analyses.
• Comparative transcriptomics/genomics: Preserves the validity of comparative studies by ensuring assemblies reflect intended biological samples.
• Transcriptome sequencing quality control: Serves as a cleaning step to prevent contaminant-driven artifacts in downstream analyses of HTS transcriptomes.

Methodology:

Analyzes assembled transcriptomes to detect and remove sequences originating from unintended sources and evaluates performance using real and simulated datasets.