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.