bio-workflows-tcr-pipeline - Route TCR/BCR repertoire data through analysis branches
Orchestrates bulk or single-cell TCR/BCR repertoire analysis from FASTQ through clonotypes, diversity, overlap, SHM, lineages, and optional specificity annotation.
Tags
Updated: 2026-10-05Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Route bulk or single-cell data
- Select MiXCR chemistry presets
- Assemble repertoire clonotypes
- Run repertoire quality control
- Normalize sequencing depth
- Calculate diversity and overlap
- Cluster BCR clones
- Reconstruct germlines and lineages
- Integrate single-cell gene expression
- Annotate antigen specificity
Inputs
- FASTQ files
- Library chemistry
- Species
- Receptor type
- Sequencing depth
- Cell-barcode data
- UMI data
- Specificity database
Outputs
- Clonotype files
- Quality-control reports
- AIRR rearrangement tables
- Depth-normalized diversity results
- Clonotype overlap results
- BCR clonal clusters
- Somatic hypermutation results
- Lineage trees
- Single-cell integration results
- Specificity annotations
- Analysis figures
Requirements
- MiXCR 4.7 or later
- Activated MiXCR license
- VDJtools 1.2.1 or later
- Immcantation suite 4.x
- scirpy 0.24 or later
- Applicable analysis tools installed
- Compatible command-line environment