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tcr-pipeline

separate

Orchestrates an end-to-end immune-repertoire pipeline from FASTQ to clonotypes, diversity, overlap, somatic hypermutation and lineages, routing on two forks. Use when deciding bulk vs single-cell (bulk amplicon/RNA-seq -> MiXCR analyze preset -> VDJtools/immunarch depth-normalized diversity and overlap -> figures; 10x paired VDJ -> MiXCR 10x preset or Cell Ranger -> scirpy gene-expression integration, chain QC, clonotype clusters); and TCR vs BCR (TCR -> exact CDR3-nt+V/J clonotypes, VDJtools diversity is fine; BCR -> somatic hypermutation makes exact clonotypes wrong -> Immcantation distToNearest/findThreshold clonal clustering, germline reconstruction, SHM, Dowser lineages); selecting the MiXCR 4.x preset by chemistry and activating its license; downsampling to equal depth before comparing diversity or overlap; and optionally annotating antigen specificity.

When to use

• bulk amplicon/RNA-seq analysis
• 10x paired VDJ analysis
• TCR exact CDR3-nt+V/J clonotypes
• BCR somatic hypermutation and clonal clustering
• depth-normalized diversity and overlap
• single-cell gene-expression integration
• MiXCR 4.x preset selection
• antigen specificity annotation

When not to use

• running BCR through exact-CDR3 VDJtools diversity

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