[User Story] QC Table
pbiology opened this issue · comments
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
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.
- Spike Stockholm clinical microbiology using is :
The unit for the above QC metrics is pair-end reads. Those QCs can be extracted from MultiQC JSON
file.