Adaptive Pipeline
The Adaptive pipeline converts data from Adaptive Biotechnologies’ ImmuneSEQ platform to AIRR (Adaptive Immune Receptor Repertoire) formatted TSV files
Web app slug: adaptive-pipeline
When to use
Section titled “When to use”Use this pipeline when you have raw data exported from the Adaptive Biotechnologies’ immunoSEQ platform and need it in AIRR format for downstream analysis (clustering, stratification, search).
Submitting a job
Section titled “Submitting a job”Navigate to Dashboard → Adaptive Pipeline → Create New Job.
Required inputs
Section titled “Required inputs”| Field | Description |
|---|---|
| Job name | A label for this run |
| Chain Type | The type of immune receptor chain (e.g., TRA, TRB, IGH) |
Optional inputs
Section titled “Optional inputs”| Field | Default | Description |
|---|---|---|
| Run pseudo-sequence alignment | false | Automatically trigger the Pseudo-Sequence Alignment DAG after conversion |
Troubleshooting
Section titled “Troubleshooting”Validation fails: missing required columns
Adaptive Biotech export formats differ by platform version. Check that Export Type is set to Clonotype (not Summary or Clone Fraction) when exporting from immunoSEQ Analyzer.
Gene names not recognized
Adaptive uses non-standard gene names (e.g., TCRBV07-02 instead of TRBV7-2). The converter handles this mapping but may not cover all edge cases. Check conversion_report.json for unmapped values.