| --- |
| license: cc-by-4.0 |
| pretty_name: refbook |
| tags: |
| - genomics |
| - reference-genome |
| - GRCh38 |
| - GRCh37 |
| - hg19 |
| - T2T-CHM13 |
| - refget |
| - seqcol |
| configs: |
| - config_name: editions |
| data_files: editions.parquet |
| - config_name: manifests |
| data_files: manifests.parquet |
| - config_name: targets |
| data_files: targets.parquet |
| - config_name: sequences |
| data_files: sequences.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, and "hg19" or "b37" as many |
| again: UCSC, Ensembl, GENCODE, the GRC'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 0.2.0 covers 55 published files, which reduce to 44 |
| **editions**: distinct sets of named sequences, whatever their order. Each edition |
| has a refbook label; the publishers' names for its files are its aliases. |
|
|
| The catalog is organized in 3 **books**, one per assembly: every release |
| of the assembly, with the sequences its editions add from outside it, and the |
| editions made from them. One set of roots serves every book: a sequence GRCh37 |
| and GRCh38 both carry (rCRS, some unplaced scaffolds, GRCh37 patches that became |
| GRCh38 alt loci) is one root. |
|
|
| | Book | Assembly | Releases | Sequences in them | Editions | Published files | |
| | --- | --- | --- | ---: | ---: | ---: | |
| | `grch37` | GRCh37 | GRCh37 – GRCh37.p13 (14) | 335 | 17 | 20 | |
| | `grch38` | GRCh38 | GRCh38 – GRCh38.p14 (15) | 711 | 13 | 17 | |
| | `t2t-chm13` | T2T-CHM13 | T2T-CHM13v1.0 – T2T-CHM13v2.0 (3) | 48 | 14 | 18 | |
|
|
| | Edition | Assembly | Published as | |
| | --- | --- | --- | |
| | `b37` | GRCh37 | 1000 Genomes `human_g1k_v37` | |
| | `b37-ebv` | GRCh37 | Broad Institute `Homo_sapiens_assembly19` | |
| | `ensembl-grch37-alt` | GRCh37 | Ensembl GRCh37 116 `Homo_sapiens.GRCh37.dna.alt` | |
| | `ensembl-grch37-chromosomes` | GRCh37 | Illumina iGenomes `Ensembl/GRCh37` | |
| | `ensembl-grch37-primary` | GRCh37 | Ensembl 75 `Homo_sapiens.GRCh37.75.dna.primary_assembly`; Ensembl GRCh37 116 `Homo_sapiens.GRCh37.dna.primary_assembly` | |
| | `ensembl-grch37-toplevel` | GRCh37 | Ensembl 75 `Homo_sapiens.GRCh37.75.dna.toplevel`; Ensembl GRCh37 116 `Homo_sapiens.GRCh37.dna.toplevel` | |
| | `gencode-grch37-p13` | GRCh37 | GENCODE 19 `GRCh37.p13.genome` | |
| | `grch37-full` | GRCh37 | GRC `GCA_000001405.14_GRCh37.p13_full_analysis_set` | |
| | `grch37-no-alt` | GRCh37 | GRC `GCA_000001405.14_GRCh37.p13_no_alt_analysis_set` | |
| | `hg19` | GRCh37 | UCSC `hg19` | |
| | `hg19-chromosomes` | GRCh37 | Illumina iGenomes `UCSC/hg19` | |
| | `hg19-p13-full-analysis-set` | GRCh37 | UCSC `hg19.p13.plusMT.full_analysis_set` | |
| | `hg19-p13-no-alt-analysis-set` | GRCh37 | UCSC `hg19.p13.plusMT.no_alt_analysis_set` | |
| | `hg19-p13-plusmt` | GRCh37 | UCSC `hg19.p13.plusMT` | |
| | `hs37d5` | GRCh37 | 1000 Genomes `hs37d5`; Illumina iGenomes `GATK/GRCh37` | |
| | `ncbi-build37.1` | GRCh37 | Illumina iGenomes `NCBI/build37.1` | |
| | `ncbi-build37.2` | GRCh37 | Illumina iGenomes `NCBI/build37.2` | |
| | `ensembl-grch38-primary` | GRCh38 | Ensembl 116 `Homo_sapiens.GRCh38.dna.primary_assembly` | |
| | `ensembl-grch38-toplevel` | GRCh38 | Ensembl 116 `Homo_sapiens.GRCh38.dna.toplevel` | |
| | `gencode-grch38-p14` | GRCh38 | GENCODE 50 `GRCh38.p14.genome` | |
| | `gencode-grch38-primary` | GRCh38 | GENCODE 50 `GRCh38.primary_assembly.genome` | |
| | `grch38-full` | GRCh38 | GRC `GCA_000001405.15_GRCh38_full_analysis_set` | |
| | `grch38-full-hs38d1` | GRCh38 | GRC `GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set` | |
| | `grch38-no-alt` | GRCh38 | GRC `GCA_000001405.15_GRCh38_no_alt_analysis_set`; Illumina iGenomes `NCBI/GRCh38` | |
| | `grch38-no-alt-hs38d1` | GRCh38 | GRC `GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set` | |
| | `grch38-no-alt-hs38d1-igenomes` | GRCh38 | Illumina iGenomes `NCBI/GRCh38Decoy` | |
| | `hg38` | GRCh38 | UCSC `hg38` | |
| | `hg38-analysis-set` | GRCh38 | Illumina iGenomes `UCSC/hg38`; UCSC `hg38.analysisSet` | |
| | `hg38-p14` | GRCh38 | UCSC `hg38.p14` | |
| | `hs38dh` | GRCh38 | 1000 Genomes `GRCh38_full_analysis_set_plus_decoy_hla`; Broad Institute `Homo_sapiens_assembly38`; Illumina iGenomes `GATK/GRCh38` | |
| | `chm13v1.0` | T2T-CHM13 | T2T consortium `chm13.draft_v1.0` | |
| | `chm13v1.1` | T2T-CHM13 | T2T consortium `chm13.draft_v1.1`; T2T consortium `chm13v2.0_noY` | |
| | `chm13v2.0` | T2T-CHM13 | Illumina iGenomes `UCSC/CHM13`; T2T consortium `chm13v2.0`; UCSC `hs1` | |
| | `chm13v2.0-dj-5s-rdna-phr-noy` | T2T-CHM13 | T2T consortium `chm13v2.0_masked_DJ_5S_rDNA_PHR_noY` | |
| | `chm13v2.0-dj-5s-rdna-phr-noy-rcrs` | T2T-CHM13 | T2T consortium `chm13v2.0_masked_DJ_5S_rDNA_PHR_noY_wi_rCRS` | |
| | `chm13v2.0-dj-5s-rdna-phr-xy` | T2T-CHM13 | T2T consortium `chm13v2.0_masked_DJ_5S_rDNA_PHR_hardMaskY` | |
| | `chm13v2.0-dj-5s-rdna-phr-xy-rcrs` | T2T-CHM13 | T2T consortium `chm13v2.0_masked_DJ_5S_rDNA_PHR_PAR_wi_rCRS` | |
| | `chm13v2.0-dj-rdna-phr-xx` | T2T-CHM13 | T2T consortium `chm13v2.masked_DJ_rDNA_PHR.forXX` | |
| | `chm13v2.0-dj-rdna-phr-xy` | T2T-CHM13 | T2T consortium `chm13v2.masked_DJ_rDNA_PHR.forXY` | |
| | `chm13v2.0-maskedY` | T2T-CHM13 | Broad Institute `chm13v2.0.maskedY`; T2T consortium `chm13v2.0_maskedY` | |
| | `chm13v2.0-maskedY-rCRS` | T2T-CHM13 | T2T consortium `chm13v2.0_maskedY_rCRS` | |
| | `chm13v2.0-maskedY-rCRS-EBV` | T2T-CHM13 | Broad Institute `chm13v2.0.maskedY.rCRS.EBV` | |
| | `chm13v2.0-refseq` | T2T-CHM13 | NCBI RefSeq `GCF_009914755.1_T2T-CHM13v2.0` | |
| | `ensembl-chm13v2.0` | T2T-CHM13 | Ensembl rapid release `Homo_sapiens-GCA_009914755.4-unmasked` | |
|
|
| ## 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 3,417 roots, with length and refget digests: every sequence of every release of each assembly (withdrawn patches included), and those editions add from outside it: the hs38d1 decoys, EBV, hg19's Yoruba mitochondrion and the hs37d5 decoy | |
| | `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 assembly report each book draws on, with its book | |
| | `aliases.parquet` | Names of each root in the GenBank, RefSeq, UCSC, GRC, Ensembl and IMGT namespaces; a name that means something only within an assembly (`chrM` is the Yoruba sequence in hg19, rCRS in hg38) carries its book | |
| | `layer_*.parquet` | Annotations in root coordinates: AGP components and gaps, alt/patch placements and the padding they give (by book: a scaffold can be placed in two assemblies), named regions (centromeres, PARs), chrY's PARs, the GRC hard-masks, IUPAC positions, N runs, NCBI soft-masking, and the masks read from published masked files where no file gives them (T2T-CHM13's acrocentric and 5S rDNA masks, named by the regions T2T-Ref's README lists) | |
| | `sequences.parquet` | The sequence store: every distinct sequence (each root, and each derivative: masked, IUPAC→N, padded or oriented), by `SQ.` digest and MD5, with the root and nucleotide operations it is made from (and, for a padded or oriented one, the book whose placement it follows) | |
| | `derivations.parquet` | Every known way to make each sequence, and the editions that use it | |
| | `editions.parquet` | Each edition: book, label, identifier (an order-independent digest of its named sequences), seqcol digest, recipe, and facets (contents, operations, naming) | |
| | `manifests.parquet` | Each edition's sequences: name, root, operations, length, MD5, `SQ.` digest | |
| | `targets.parquet` | Each published file: its edition, publisher, name, URL and seqcol digest | |
| | `target_sequences.parquet` | Each published file's order of sequences | |
| | `collections/*.json` | Seqcol (level 2) documents for every edition and published file, named by digest | |
| | `evidence/` | What each published file was observed to contain, the source locks, and the root verification reports | |
| | `catalog.json` | The release manifest: every file's size, sha256 and role | |
|
|
| Four nucleotide operations make every derivative. Two write `N` and keep |
| coordinates: a **mask** (a layer's spans: the GRC hard-mask, chrY's PARs) and |
| **IUPAC→N**. Two lay an alt scaffold or patch out by its placement on its |
| parent: **pad** writes it in the parent's coordinates, `N` before and after, as |
| Ensembl's GRCh37 files do; **orient** only reverse-complements one placed on |
| the minus strand, as GENCODE 19 does. |
|
|
| Read any table directly with DuckDB, Polars or pyarrow, for example: |
|
|
| ```python |
| import polars as pl |
| base = "https://huggingface.co/datasets/abdenlab/refbook/resolve/v0.2.0/" |
| m = pl.read_parquet(base + "manifests.parquet") |
| m.filter(pl.col("name") == "chr21").select("edition", "md5", "operations").unique("md5") |
| ``` |
|
|
| The `refbook` Python library (github.com/abdenlab/refbook) identifies a header |
| against this catalog, and resolves, materializes and fetches any collection |
| whose sequences it holds. |
|
|
| ## 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 |
| one root with no INSDC record, the hs37d5 decoy (`1000G:hs37d5`), is 1000 |
| Genomes' concatenation of segments of other sequences, with its make-up as its |
| AGP. 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 (`v0.2.0`, …). Pin URLs to a tag, for example |
| `https://huggingface.co/datasets/abdenlab/refbook/resolve/v0.2.0/catalog.json`. |
|
|
