FASTQ Pipeline

The FASTQ pipeline accepts raw FASTQ sequencing files and performs full immune repertoire analysis with — producing V(D)J gene annotations, clonotypes, and alignment reports.

Web app slug: fastq-pipeline

When to use

Use this pipeline when you have raw FASTQ files from bulk TCR or BCR sequencing experiments and want AIRR-formatted output.

Submitting a job

Navigate to Dashboard → FASTQ Pipeline → Create New Job.

Required inputs

Field	Description
Patient Label	Label for the donor
Chain Type	The type of immune receptor chain (e.g., TRA, TRB, IGH)
Preset	Some pre saved configuration for sequencing parameters
AIRR Mode	The mode for AIRR formatting
Upload files	Zipped one or more`.fastq.gz` files.

Advanced Configurations

These fields are only applied when Override Config is enabled.

Field	Default	Options / Notes
Species	(from preset)	`hsa` (human), `mmu` (mouse)
Starting Material	(from preset)	`rna`, `dna`
UMI Tag Pattern	—	UMI tag pattern string; only relevant for `generic-amplicon-with-umi` presets
Auto Assemble	`true`	Automatically selects Assemble By and Impute Missing based on FastP read-length metrics; also enables FastP and QC Plots
Assemble Clonotypes By	(auto)	`CDR3`, `[CDR1,CDR2,CDR3]`, `VDJRegion`, `{CDR1Begin:CDR3End}`, `{CDR1Begin:FR4End}` — the receptor region used to define a clonotype
Split By C	(from preset)	`enable` — treats IGH clonotypes with identical sequences but different C genes as distinct; `disable` — merges them
Impute Missing Clonotypes	`false`	When enabled, retains clonotypes with missing CDR1 or CDR2; when disabled those rows are dropped
QC Plots	`false`	Generates PDF charts for alignment rates, chain usage, and read coverage
FastP	`false`	Runs FastP on input FASTQ files and outputs `fastp.html` / `fastp.json` quality reports
CPU Threads	`4`	Number of CPU threads to be used
Extra Params	—	Any additional flags passed

Output files

File	Description
`results.zip`	Archive of all output files