BCR Sequencing

B cell receptor sequencing reads the immunoglobulin genes of a sample and turns them into a catalogue of antibodies. The catalogue answers questions that flow cytometry and serology cannot: which V genes the response recruited, how much the sequences have mutated from their germline templates, and whether individual clones expanded in response to the antigen you care about. This section works through the method from both ends, the wet lab that shapes what you can measure, and the analyses that turn annotated sequences into biology.

Every number and table on these pages comes from a real run of the code shown on the page, inside one pinned container, on committed example data shaped exactly like the AIRR tables that nf-core/airrflow produces. The companion repository holds the runners and the fixtures.

The path

Page	What it covers
What is BCR sequencing	antibody structure, V(D)J recombination, somatic hypermutation and clonotypes
Library Prep & Sequencing	amplicon PCR versus 5’RACE, UMIs, bulk versus single-cell, sequencing platforms
Repertoire Analysis	V(D)J assignment, CDR3 properties, SHM, clonal and diversity analysis
Running nf-core/airrflow	the pipeline from FASTQ to annotated clonotypes, and what to compute downstream

The data

One small table stands in for airrflow output in the worked example: an immunoglobulin heavy-chain table for one sample, with IMGT gene calls, CDR3 sequences, isotypes, mutation frequencies and clone identifiers. It is synthetic and deterministic, so the page rebuilds bit for bit, but its columns are the columns a real run writes. When a page quotes a number, the container run beside the code produced it.