[User Story] QC Table

[pbiology]

Need

As a clinician I want a table which shows QC metrics for a given sample/case so I can quickly understand if the sample is good enough.

Suggested approach

This could be a table showing at least the following stats.

• Total bases
• The number of raw reads
• Trimmed reads
• Filtered reads
• Reads mapped to the host genome (human)
• Input reads for classifiers
• Unclassified reads
• Reads assigned to Homo sapiens, fungi, archaea, bacteria and viruses, respectively.

Can be closed when

• [ ] Endpoint serving up the suggested QC metrics
• [ ] The front end shows the QC metrics in a easy to understand way

Blockers

No response

Anything else?

No response

[LilyAnderssonLee]

There are some updates regarding QC table:

• Total reads
• Total reads after filtering
• Human mapped reads
• Human kraken reads
• % total human reads (mapped+kraken/total reads after filtering)
• % Bacterial reads (of total reads after filtering)
• % Virus reads (of total reads after filtering)
• % Eukaryote reads (of total reads after filtering)
• % Other reads (of total reads after filtering)
• % Unclassified reads (of total reads after filtering)
• %spike reads (of total reads after filtering)
  • Spike Stockholm clinical microbiology using is : Emesvirus zinderi
  • Spikes vary among labs or protocols, so a spikes list can be provided.

The unit for the above QC metrics is pair-end reads. Those QCs can be extracted from MultiQC JSON file.