Description

A module to translate BCR and TCR nucleotide sequences into amino acid sequences using amulety and igblast.

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

tsv:file

TSV with BCR/TCR nucleotide sequences in AIRR rearrangement format

*.{tsv}

reference_igblast:file

Built reference databases for igblast

Output

name:type
description
pattern

repertoire_translated

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*_translated.tsv:file

TSV with BCR/TCR amino acid sequences in AIRR rearrangement format

*.tsv

versions

versions.yml:file

File containing software versions

versions.yml

Tools

amulety
GPL v3

Python package to create embeddings of BCR and TCR amino acid sequences.

amulety.readthedocs.io/en/latest https://github.com/immcantation/amulety 10.1101/2025.03.21.644583

igblast
United States Government Work

A tool for immunoglobulin (IG, BCR) and T cell receptor (TCR) V domain sequences blasting.

ncbi.nlm.nih.gov/igblast ncbi.github.io/igblast https://github.com/ncbi/igblast 10.1093/nar/gkt382
included in
airrflow
maintainer
Github user ggabernet
get in touch
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