| --- |
| license: cc-by-4.0 |
| pretty_name: refbook |
| tags: |
| - genomics |
| - reference-genome |
| - GRCh38 |
| - refget |
| - seqcol |
| configs: |
| - config_name: flavor_sequences |
| data_files: flavor_sequences.parquet |
| - config_name: recipes |
| data_files: recipes.parquet |
| - config_name: roots |
| data_files: roots.parquet |
| - config_name: aliases |
| data_files: aliases.parquet |
| --- |
| |
| # refbook |
|
|
| **One catalog for the many published versions of the human reference genome.** |
|
|
| "GRCh38" names dozens of different FASTA files: UCSC, Ensembl, GENCODE, NCBI's |
| analysis sets, Broad/GATK, 1000 Genomes, iGenomes. They differ in which sequences |
| they contain, how they name and order them, and whether some bases are masked or |
| rewritten. refbook describes every one of them as a **recipe** applied to the same |
| **roots**, the original INSDC sequences, and counts a version as cataloged only |
| when its recipe reproduces the published file sequence by sequence. |
|
|
| Release 0.1.0 covers 17 published GRCh38 files, which reduce to 13 |
| distinct sequence sets. |
|
|
| | Publisher | Files reproduced | |
| | --- | --- | |
| | Broad / 1000 Genomes | GRCh38_full_analysis_set_plus_decoy_hla, Homo_sapiens_assembly38 | |
| | Ensembl 116 | primary_assembly, toplevel | |
| | GENCODE 50 | p14, primary_assembly | |
| | GRC (NCBI analysis sets) | full, full + hs38d1, no_alt, no_alt + hs38d1 | |
| | Illumina iGenomes | GATK/GRCh38, NCBI/GRCh38, NCBI/GRCh38Decoy, UCSC/hg38 | |
| | UCSC | hg38, hg38.analysisSet, hg38.p14 | |
|
|
| ## What is in it |
|
|
| All coordinates are 0-based, half-open. Sequence digests follow GA4GH refget |
| (MD5 and `SQ.` sha512t24u); collection digests follow GA4GH seqcol. |
|
|
| | File | Contents | |
| | --- | --- | |
| | `roots.parquet` | The 3,097 roots: GRCh38 p0–p14 (711 sequences), the hs38d1 decoys (2,385) and EBV, with length and refget digests | |
| | `roots_external.parquet` | IMGT/HLA 3.18.0 alleles, by identifier and digest only (see below) | |
| | `root_blocks.parquet` | The bases of every root, uppercase with IUPAC codes kept, in 64 kb blocks, laid out for HTTP range reads | |
| | `assembly_members.parquet` | Every row of every GRCh38 and hs38d1 assembly report | |
| | `aliases.parquet` | Names of each root in the GenBank, RefSeq, UCSC, GRC, Ensembl and IMGT namespaces | |
| | `layer_*.parquet` | Annotations in root coordinates: AGP components and gaps, alt/patch placements, named regions (centromeres, PARs), the GRC hard-masks, IUPAC positions, N runs, NCBI soft-masking | |
| | `recipes.parquet` | Each published file's recipe and seqcol digest | |
| | `flavor_sequences.parquet` | Each published file's sequences in order: name, root, length, MD5, `SQ.` digest | |
| | `family_tree.json` | How the files relate: each one's nearest relative and the exact difference | |
| | `seqcol/*.json` | A seqcol (level 2) document per published file | |
| | `evidence/` | What each published file was observed to contain, and the root verification reports | |
| | `catalog.json` | The release manifest: every file's size, sha256 and role | |
|
|
| Read any table directly with DuckDB, Polars or pyarrow, for example: |
|
|
| ```python |
| import polars as pl |
| base = "https://huggingface.co/datasets/abdenlab/refbook/resolve/v0.1.0/" |
| fs = pl.read_parquet(base + "flavor_sequences.parquet") |
| fs.filter(pl.col("name") == "chr21").select("flavor", "md5").unique("md5") |
| ``` |
|
|
| A Python library that identifies a header against this catalog and fetches bases |
| by region is in development. |
|
|
| ## Sources and licensing |
|
|
| The catalog tables are released under CC-BY-4.0. The underlying sequences are |
| INSDC records (GenBank), distributed by NCBI without restrictions on use. The |
| published files used as reproduction targets belong to their publishers and are |
| not redistributed here; the `evidence/` tables record only their sequence names, |
| lengths and digests. |
|
|
| IMGT/HLA alleles are not redistributed. The IPD-IMGT/HLA Database is licensed |
| under CC BY-NoDerivs, and its maintainers ask not to be mirrored. This catalog |
| records only allele identifiers, names and digests, with links to the IMGT/HLA |
| release. If you use the HLA entries, please cite IPD-IMGT/HLA (Barker et al., |
| *Nucleic Acids Research* 2026; Robinson et al., *Tissue Antigens* 2000). |
|
|
| ## Versions |
|
|
| Each release is a tag (`v0.1.0`, …). Pin URLs to a tag, for example |
| `https://huggingface.co/datasets/abdenlab/refbook/resolve/v0.1.0/catalog.json`. |
|
|
