Sequencing Runs
A sequencing run represents a single run on a sequencing instrument. Runs contain metadata about the sequencing process and link to the read files generated for each sample.
Run Metadata
Each sequencing run tracks:
| Field | Description |
|---|---|
| Run ID | Unique identifier for the run |
| Run Name | Optional descriptive name |
| Platform | Sequencing platform used |
| Instrument | Specific instrument model |
| Run Date | Date the run was performed |
| Folder Path | Path to the run output directory |
Quality Metrics
Runs can include quality control metrics:
| Metric | Description |
|---|---|
| Q30 Score | Percentage of bases with quality score ≥ 30 |
| Cluster Density | Clusters per square millimeter |
| Pass Filter % | Percentage of clusters passing quality filter |
| Total Reads | Total number of reads generated |
| Total Bases | Total number of bases sequenced |
MultiQC Reports
If a MultiQC report is available for the run, it is linked in the multiQcReport
field. MultiQC aggregates quality metrics from multiple tools (FastQC, fastp,
etc.) into a single interactive HTML report.
Reads
Reads are the sequencing files linked to individual samples within a run:
| Field | Description |
|---|---|
| file1 | Path to forward reads (R1) |
| file2 | Path to reverse reads (R2, paired-end only) |
| checksum1/checksum2 | MD5 checksums for file integrity |
| readCount1/readCount2 | Number of reads per file |
| avgQuality1/avgQuality2 | Average quality score per file |
| fastqcReport1/fastqcReport2 | Paths to per-file FastQC reports |
Read-Sample Linking
Reads are linked to samples through the sampleId field. Each read record
connects a pair of FASTQ files to the sample they came from. A sample can have
multiple read records (e.g., from multiple sequencing runs or lanes).
ENA Accessions
After ENA submission, reads receive accession numbers:
experimentAccessionNumber— the ENA experiment accession (ERX…)runAccessionNumber— the ENA run accession (ERR…)
These are assigned during the ENA submission process.
Order Pipelines and Read Writeback
Order pipelines operate directly on these linked reads and write selected
results back to the canonical Read record. This keeps downstream QC,
validation, and submission workflows aligned on the same file metadata.
Current built-in writeback behavior:
| Pipeline | What it updates on Read |
|---|---|
| Simulate Reads | file1, file2, readCount1, readCount2 |
| FASTQ Checksum | checksum1, checksum2 |
| FastQC | fastqcReport1, fastqcReport2, readCount1, readCount2, avgQuality1, avgQuality2 |
Run-level outputs such as summaries, reports, and archives are still stored as
pipeline artifacts linked to the corresponding run. The sequencing UI then uses
both the canonical Read fields and these artifacts to present per-sample QC
status for an order.