plate-qc

A pipeline for assessing cross-contamination in high throughput metagenomic sequencing, and guidelines for upstream preventative measures.

Metrics/Tasks

All are calculated at kmer-level for greatest applicability and computational efficiency

0. Count kmers
1. Row-wise and column-wise cross-correlation
2. Negative control (blank) similarity to other samples
3. Positive control (natural sample) similarity to previous independent runs
4. Positive control (defined sample) similarity to previous independent runs
5. What else?