A pipeline for assessing cross-contamination in high throughput metagenomic sequencing, and guidelines for upstream preventative measures.
All are calculated at kmer-level for greatest applicability and computational efficiency
- Count kmers
- Row-wise and column-wise cross-correlation
- Negative control (blank) similarity to other samples
- Positive control (natural sample) similarity to previous independent runs
- Positive control (defined sample) similarity to previous independent runs
- What else?