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antigenomicsantigenomicsOfficial·1 Agent Skills Included

arda

Fast TCR and BCR immune receptor sequence annotation

Annotates T-cell and B-cell receptor sequences with framework and CDR regions, V/D/J gene calls, and isotype assignments. Eliminates slow per-batch IgBLAST runs by mapping sequences against a pre-built germline reference with MMseqs2 and a C++ projection step. Repairs bare CDR3 records, extracts clonotypes from bulk RNA-seq, and outputs spec-valid AIRR tables for downstream immunology analysis.
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npx skills add antigenomics/arda --all -g -y
Available:

Gives the agent the repository layout, build and test commands, and correctness rules for working on the arda annotation codebase.

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antigenomicsantigenomics

arda

Annotate TCR/BCR sequences using IgBLAST and MMseqs2 reference databases.

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Frequently Asked Questions

FAQPage Schema
How to install arda?▼

Run `npx skills add antigenomics/arda --all -g -y` in your terminal to install this skill globally.

What does arda do?▼

It annotates TCR and BCR sequences with FR1-4 and CDR1-3 regions, V/D/J gene calls, and isotypes, producing spec-valid AIRR output much faster than IgBLAST.

Can arda analyze bulk RNA-seq data?▼

Yes. The `arda rnaseq` mode filters receptor reads from paired FASTQ files, assembles long CDR3s, and collapses errors into clonotype tables.

Which organisms does arda support?▼

Human and mouse get full TCR and BCR loci, while rat, rabbit, and rhesus monkey are supported for immunoglobulin loci only.

Do I need to install IgBLAST or MMseqs2 separately?▼

No. A plain pip install auto-fetches the curated reference database and a static MMseqs2 binary on first use, and IgBLAST is only needed to rebuild references.

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