arda

What problem does it solve?

This Skill solves the problem of accurately and efficiently annotating TCR and BCR sequences, providing framework/CDR regions, V/D/J gene calls, constant-region isotype, junction/CDR3 boundaries, and AIRR output for both nucleotide and amino-acid inputs.

Core Features & Use Cases

• TCR/BCR Annotation: Annotates framework and complementarity-determining regions of TCR and BCR sequences.
• IgBLAST Work: Performs the expensive IgBLAST work offline, building a pre-aligned reference database.
• MMseqs2 Mapping: Maps sequences to the reference database using MMseqs2 for fast annotation.
• Use Case: An immunologist uses this Skill to annotate TCR sequences from a bulk RNA-seq experiment, obtaining germline and junction information for each sequence.

Quick Start

Use the arda skill to annotate TCR sequences from a bulk RNA-seq experiment.