Fast TCR/BCR FR/CDR region annotation (Antigen Receptor Domain Annotation). Use whenever the user wants to annotate immune-receptor sequences with framework/CDR regions, V/D/J gene calls, constant-region isotype (ccall/cclass), junction/CDR3 boundaries, or AIRR output — for TCR (TRA/TRB/TRG/TRD) or BCR (IGH/IGK/IGL), nucleotide or amino acid, single sequences or large FASTA/FASTQ. Also use for: marking up, validating or REPAIRING a bare (CDR3 amino acid, V, J) record that has no read behind it — a VDJdb-style row — including locating where it disagrees with germline and restoring a missing Cys104 / Phe118 anchor; calling the D gene (and tandem D-D) on a bare junction, or inferring it from junction length when the protein shows none of it; extracting the receptor repertoire (clonotypes, isotype usage) from bulk RNA-seq; getting germline FR1-FR3/CDR1-CDR2 (V) or FR4 (J) subsequences for individual alleles; building or rebuilding the reference database from IMGT germlines via IgBLAST; or diagnosing mmseqs2 setup. arda runs MMseqs2 + a C++ coordinate projection (IgBLAST is offline/build-time only), so it is much faster than IgBLAST at annotation time. Load references/ files for the detailed API, region/junction semantics, reference-build pipeline, or mmseqs install/troubleshooting.
Install with
Claude CodeCodexCursorGitHub CopilotGemini CLI
Supported by the Atlas install prompt. Skill-specific requirements vary.
Skill stats
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About this skill
Fast TCR/BCR FR/CDR region annotation (Antigen Receptor Domain Annotation). Use whenever the user wants to annotate immune-receptor sequences with framework/CDR regions, V/D/J gene calls, constant-region isotype (ccall/cclass), junction/CDR3 boundaries, or AIRR output — for TCR (TRA/TRB/TRG/TRD) or BCR (IGH/IGK/IGL), nucleotide or amino acid, single sequences or large FASTA/FASTQ. Also use for: marking up, validating or REPAIRING a bare (CDR3 amino acid, V, J) record that has no read behind it — a VDJdb-style row — including locating where it disagrees with germline and restoring a missing Cys104 / Phe118 anchor; calling the D gene (and tandem D-D) on a bare junction, or inferring it from junction length when the protein shows none of it; extracting the receptor repertoire (clonotypes, isotype usage) from bulk RNA-seq; getting germline FR1-FR3/CDR1-CDR2 (V) or FR4 (J) subsequences for individual alleles; building or rebuilding the reference database from IMGT germlines via IgBLAST; or diagnosing mmseqs2 setup. arda runs MMseqs2 + a C++ coordinate projection (IgBLAST is offline/build-time only), so it is much faster than IgBLAST at annotation time. Load references/ files for the detailed API, region/junction semantics, reference-build pipeline, or mmseqs install/troubleshooting.
Quick start
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Fast TCR/BCR FR/CDR region annotation (Antigen Receptor Domain Annotation). Use whenever the user wants to annotate immune-receptor sequences with framework/CDR regions, V/D/J gene calls, constant-region isotype (c_call/c_class), junction/CDR3 boundaries, or AIRR output — for TCR (TRA/TRB/TRG/TRD) or BCR (IGH/IGK/IGL), nucleotide or amino acid, single sequences or large FASTA/FASTQ. Also use for: marking up, validating or REPAIRING a bare (CDR3 amino acid, V, J) record that has no read behind it — a VDJdb-style row — including locating where it disagrees with germline and restoring a missing Cys104 / Phe118 anchor; calling the D gene (and tandem D-D) on a bare junction, or inferring it from junction length when the protein shows none of it; extracting the receptor repertoire (clonotypes, isotype usage) from bulk RNA-seq; getting germline FR1-FR3/CDR1-CDR2 (V) or FR4 (J) subsequences for individual alleles; building or rebuilding the reference database from IMGT germlines via IgBLAST; or diagnosing mmseqs2 setup. arda runs MMseqs2 + a C++ coordinate projection (IgBLAST is offline/build-time only), so it is much faster than IgBLAST at annotation time. Load references/ files for the detailed API, region/junction semantics, reference-build pipeline, or mmseqs install/troubleshooting.
About this listing
Category
General
Reported license
GPL-3.0
Listing language (estimated)
English
Review status
Not individually reviewed
Agent compatibility
Atlas installation supports Claude Code, Codex, and Cursor. Skill-specific dependencies and features are checked during setup.
Claude Code
Codex
Cursor
GitHub Copilot
Gemini CLI