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contamination-screening

separate

Detects contamination in sequencing reads - cross-species (FastQ Screen, Kraken2), vector/PhiX/adapter, rRNA, and same-species cross-sample/index-hopping and sample swaps (SNP fingerprints via verifyBamID2/NGSCheckMate/somalier). Use when suspecting cross-contamination, PDX host reads, microbial carry-over, or sample swaps, and to decide whether to report, filter, or align to a combined reference. For deep taxonomic profiling use metagenomics/kraken-classification.

When to use

• cross-species contamination detection
• vector/PhiX/adapter contamination
• rRNA over-representation
• same-species cross-sample contamination
• index-hopping detection
• sample swap detection
• PDX host reads
• microbial carry-over

When not to use

• deep taxonomic profiling
• metagenomics/kraken-classification
• metagenomics/metaphlan-profiling
• rRNA depletion as an RNA prep metric
• read-qc/rnaseq-qc
• adapter removal
• read-qc/adapter-trimming

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