mehari-data

Reproducible data builds for mehari.

This repository contains a snakemake workflow to build mehari transcript databases based on SACGF/cdot.

Resulting Files

Databases are built for each combination of genome release (GRCh37, GRCh38) and reference source (ensembl, refseq), once for each source release listed in config/config.yaml:

• mehari-data v0.14.0
  • uses:
    • mehari v0.47.0
    • cdot: v0.2.36
  • GRCh37-refseq-105.20220307
    • genome release: GRCh37.p13
    • RefSeq annotation release: 105.20220307
    • RefSeq assembly: GCF_000001405.25
    • resulting transcript database: mehari-data-txs-GRCh37-refseq-105.20220307-0.14.0.bin.zst
  • GRCh37-ensembl-87
    • genome release: GRCh37.p13
    • VEP/ENSEMBL release: 87
    • RefSeq equivalent: GCF_000001405.25
    • resulting transcript database: mehari-data-txs-GRCh37-ensembl-87-0.14.0.bin.zst
  • GRCh38-refseq-RS_2025_08
    • genome release: GRCh38.p14
    • RefSeq annotation release: RS_2025_08
    • RefSeq assembly: GCF_000001405.40
    • resulting transcript database: mehari-data-txs-GRCh38-refseq-RS_2025_08-0.14.0.bin.zst
  • GRCh38-ensembl-115 and GRCh38-ensembl-116
    • genome release: GRCh38.p14
    • VEP/ENSEMBL release: 115 and 116
    • RefSeq equivalent: GCF_000001405.40
    • resulting transcript databases: mehari-data-txs-GRCh38-ensembl-115-0.14.0.bin.zst and mehari-data-txs-GRCh38-ensembl-116-0.14.0.bin.zst
  • GRCh37-ensembl-87-and-refseq-105.20220307 and GRCh38-ensembl-116-and-refseq-RS_2025_08
    • the newest listed Ensembl and RefSeq databases of a genome release, merged
    • resulting transcript databases: mehari-data-txs-GRCh37-ensembl-87-and-refseq-105.20220307-0.14.0.bin.zst and mehari-data-txs-GRCh38-ensembl-116-and-refseq-RS_2025_08-0.14.0.bin.zst

Up to v0.13.0, the databases were named mehari-data-txs-{genome release}-{ensembl,refseq,ensembl-and-refseq}-{version}.bin.zst, with one release per source.

New builds of mehari-data will be considered when

• a new mehari version is released, OR
• a new cdot version is released, OR
• bugs are found and make a new release necessary.

Generally, only the data for the latest mehari protobuf schema is created.