TCR-BCR-nf

Pipeline to genotype Tcell and Bcell receptors from bulk or single-cell RNA-seq data

Description

This pipeline calls software TRUST4 to genotype T cell and B cell receptors.

Dependencies

1. This pipeline is based on nextflow. As we have several nextflow pipelines, we have centralized the common information in the IARC-nf repository. Please read it carefully as it contains essential information for the installation, basic usage and configuration of nextflow and our pipelines.
2. External software:

• TRUST4

You can avoid installing all the external software by only installing Docker and using the official TRUST4 docker container (at quay.io/biocontainers/trust4:, see tags at https://quay.io/repository/biocontainers/trust4?tab=tags). See the IARC-nf repository for more information. Note that TRUST4 requires references files IMGT+C.fa and bcrtcr.fa, that can be generated using perl scripts from the trust4 git repository:

perl BuildImgtAnnot.pl Homo_sapien > IMGT+C.fa
grep ">" IMGT+C.fa | cut -f2 -d'>' | cut -f1 -d'*' | sort | uniq > bcr_tcr_gene_name.txt  
perl BuildDatabaseFa.pl reference.fa annotation.gtf bcr_tcr_gene_name.txt > bcrtcr.fa

Input

Type	Description
input_folder	Folder with bam files to be processed

Parameters

• Mandatory

Name	Example value	Description
--IMGTC_fasta	IMGT+C.fa	fasta file of reference genome from the international ImMunoGeneTics information system [file human_IMGT+C.fa from https://github.com/liulab-dfci/TRUST4]
--bcrtcr_fasta	bcrtcr.fa	fasta file with reference BCR and TCR regions [see https://github.com/liulab-dfci/TRUST4 for generation]

• Optional

Name	Default value	Description
--barcode	None	Run trust4 using a specific barcode (for single cell data only, usually BC for CellRanger output)

• Flags

Flags are special parameters without value.

Name	Description
--help	Display help

Usage

nextflow run iarcbioinfo/TCR-BCR-nf --input_folder bams --IMGTC_fasta TRUST4/IMGT+C.fa --bcrtcr_fasta TRUST4/bcrtcr.fa --barcode BC

Output

Type	Description
TRUST_*_barcode_report.tsv	Report with inferred cell type and TCR and BCR genotypes
TRUST_*_report.tsv	Report with proportion of each TCR and BCR genotype

Contributions

Name	Email	Description
Nicolas Alcala*	[email protected]	Developer to contact for support

References

Song, L., Cohen, D., Ouyang, Z. et al. TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data. Nat Methods 18, 627–630 (2021). https://doi.org/10.1038/s41592-021-01142-2