QC metrics - Snitkin-Lab-Umich/nanoQC GitHub Wiki

The final summary report includes key quality control (QC) metrics for each sample:

• Coverage: Calculated as

coverage = (number_of_reads_nanoplot × mean_read_length_nanoplot) / total_length_medaka_quast

This estimates the sequencing depth for each assembly.

• QC Check Status: Each sample receives a PASS or FAIL based on two criteria:

  • Coverage must be greater than 30×.
  • The number of contigs (from QUAST) must be less than 20. Only samples meeting both criteria are marked as PASS; otherwise, they are marked as FAIL.

These metrics are found in the columns coverage and qc_check in the final summary file ({prefix}_report.csv).