refbox¶
Build standardized, indexed reference files for genome browsers — in one command.
refbox turns a YAML registry of species/assemblies into ready-to-load browser
inputs, and can also build static, backend-free search indexes for in-browser
gene/transcript lookup.
What it produces¶
| Resource | Output |
|---|---|
| Genome FASTA | bgzip + samtools faidx (.fa.gz + .fai + .gzi) + chrom.sizes |
| Transcriptome FASTA | bgzip + faidx (auto-derived from genome + GTF when no upstream URL exists) |
| GTF / GFF3 annotations | sorted + bgzip + tabix |
| Repeats | UCSC RepeatMasker rmsk.txt.gz → BED + GTF; .fa.out.gz report |
| RNAcentral ncRNAs | direct download or liftover from another assembly |
| ENCODE SCREEN cCREs | sorted + bgzip + tabix |
| UCSC cytogenetic bands | tabix BED + bigBed ideogram |
Full Index (.rba) |
SQLite + FTS5 + trigram + annotation structure — exact / prefix / fuzzy / alias search and rendering |
Lite Index (.rbi) |
compact SQLite B-tree lookup — fast name→position autocomplete |
It ships a registry of 26 species / 42 assemblies (human, mouse, rat, dog, cow, pig, chimp, gorilla, zebrafish, fly, worm, sea urchin, yeast, plants, bacteria, viruses…) covering GENCODE, Ensembl, Ensembl Genomes, UCSC golden path, NCBI, RNAcentral, and ENCODE SCREEN.
Command surface¶
refbox download # only fetch raw files configured in species.yaml
refbox pull # full pipeline: download (if missing) + build + test + publish
refbox publish # flatten an existing build/ tree to <Assembly>.<name>
refbox test # validate build/ outputs
refbox build # single-file / directory build for arbitrary inputs
Where to go next¶
- :material-download: **[Installation](installation.md)** — pip + external bioinformatics tools.
- :material-rocket-launch: **[Quick Start](quickstart.md)** — the most common workflows.
- :material-console: **[Pipeline Commands](commands/pipeline.md)** — `download` / `pull` / `publish` / `test`.
- :material-file-cog: **[Build Command](commands/build.md)** — build any file or directory by hand.
- :material-database-search: **[Full Index `.rba`](indexes/rba.md)** — FTS5 search + annotation structure.
- :material-database: **[Lite Index `.rbi`](indexes/rbi.md)** — compact name→position lookup.
Looking for how to build a search index?
The short answer: refbox build -rba ANNOT.gtf.gz -o OUT.rba (full index) or
refbox build -rbi ANNOT.gtf.gz -o OUT.rbi (lite index). See
Full Index and Lite Index.