GenAIRR
Fast simulator of BCR and TCR sequences with full ground-truth annotations: V(D)J recombination, somatic hypermutation and sequencing artifacts across 23 species. Rust core with a Python API, for training and benchmarking AIRR-seq tools
What XERJ indexed
Snapshot
The whole repository at commit 18ecdf6e9b (2026-10-20). master is 335 commits ahead.
Selected work
“preserve duplex truth through clonal families”. 32 files, 5,465 lines in audit-docs, engine_rs, tools.
Licence
The repository
LICENSE file checked at the pinned commit; the author agreed to inclusion.
The XERJ corpus
The author agreed by email on 2026-10-24. Agents read it for how it works, not to copy it. Answers name the repo, the commit and the file:line.
selected for the XERJ Corpus Hublicence clearedsuggested use: approach only
airr-seqbcrbenchmarkingbioinformaticscomputational-biologyimmune-repertoireimmunoglobulinimmunoinformatics
Example questions
- How does GenAIRR implement airr-seq?
- Where does GenAIRR handle “preserve duplex truth through clonal families”?
- What does audit-docs do in GenAIRR?
Inside the indexed corpus
- 915 files, 53.3 MB in total, about 59.6 KB per file.
- The selected commit changed 32 of those files (3.5%).
- Languages by size: Python 55.1%, Rust 38.1%, HTML 5.1%, CSS 1.2%, JavaScript 0.4%.
- On GitHub since 2024-03-02, last push 2026-10-31, 719 commits on master.
- The pin is 335 commits behind master; the corpus answers from the pinned code, not the newest.
Licence on GitHub and in the corpus
GitHub reported GPL-3.0 for MuteJester/GenAIRR on 2026-10-31, and the LICENSE file at commit 18ecdf6e9b was reviewed as GPL-3.0. They match, so answers from this corpus carry the same terms as the live repository.
Contributors
Thomas Konstantinovsky (@MuteJester) has 1 selected repository on the hub.
Using XERJ with GenAIRR
- Ask questions about a GitHub repo without cloning it
- Index a reference library for a coding agent
- ripgrep vs a code index for coding agents: 30 tasks
- Best MCP servers for local code search in 2026, compared
The prompt
Paste it into your AI agent. It clones MuteJester/GenAIRR at the pinned commit and indexes it on your machine.
Search the GitHub repository MuteJester/GenAIRR with XERJ (https://hub.xerj.org/corpus/mutejester--genairr). Run these in a shell, in order, and check each result before the next: 1. xerj --help (success: it prints usage). If xerj is missing: curl -fsSL https://xerj.org/get | sh 2. git clone https://github.com/MuteJester/GenAIRR GenAIRR && git -C GenAIRR checkout 18ecdf6e9bb180712e0f61f12cdbe55706775ee5 3. Start a local node and leave it running: xerj --insecure --data-dir ./xerj-data 4. xerj autoindex ./GenAIRR --url http://127.0.0.1:9200 --prefix genairr --progress plain 5. xerj autoindex map --url http://127.0.0.1:9200 Then answer my question from the indexed files and cite the ax_path of every hit. Query syntax: https://xerj.org/llms.txt Licence: GPL-3.0. Read it for the approach only, do not copy code.
Related
Thomas KonstantinovskyHealth and clinical reference corporasyntheascispacydistilabeldavewalker5/MolecularClockSimulationscikit-bio/scikit-biodavewalker5/OctopusController
Stats: GitHub API, fetched 2026-10-31. Snapshot: the git tree at the pinned commit. Selected work and consent: the XERJ registry.