BCRseq / TCRseq analysis

To perform bulk amplicon BCRseq / TCRseq data analysis you can use the nf-core/airrflow pipeline. To perform single-cell BCRseq / TCRseq data analysis with data generated with the 10x genomics chromium (e.g. immune profiling libraries or similar), you will have to run the nf-core/scrnaseq pipeline first running the cellranger-multi subworkflow. Afterwards, you can use the nf-core/airrflow pipeline departing from the AIRR format tables provided as output by cellranger multi to perform downstream analysis.

nf-core/airrflow pipeline

The latest stable release is -r 3.0.0.

A typical command to run the pipeline is as follows:

nextflow run nf-core/airrflow -r 3.0.0 \
-profile cfc \
--input samplesheet.tsv \
--library_generation_method specific_pcr_umi \
--cprimers CPrimers.fasta \
--vprimers VPrimers.fasta \
--umi_length 12 \
--outdir ./results

Please familiarize yourself with the nf-core/airrflow documentation on the nf-core website before running the pipeline. It also contains documentation on how to create the samplesheets.