# Archives & Bulk Data

The cold-storage, citable layer: raw reads, the full variant archive, and permanent DOIs — for when you need the underlying data rather than an interactive query.

## README — accessions & what's there

Resource | Accession / DOI | Contents
--- | --- | ---
NCBI BioProject | PRJNA954521 | 9K-RGP clean sequencing data
NCBI BioProject | PRJNA597070 | 3K-RGP data
NCBI BioProject | PRJNA952097 | PacBio HiFi for IR64RS2
European Variation Archive | PRJEB105137 | Variants — SNP set ERZ28769989, InDel set ERZ28769990
KAUST repository | DOI 10.25781/N3AF-NP78 | Raw reads (permanent handle)

Use this when… you need raw FASTQ/gVCF, the complete variant archive, or a permanent citable handle — not for interactive queries.

## Tutorial — fetch from the archives

1. Locate the accession (above) at the EVA/ENA or NCBI SRA.
2. Download via the archive's interface or command-line tools.
3. Verify checksums before use.

## Workflow — get a VCF, then slice it locally

Goal: get the genome-wide SNP VCF for one reference from the EVA, then slice a region locally with tabix (bridging to efficient access).

## Examples

    # Download a variant file by accession, then index for tabix
    wget https://ftp.ebi.ac.uk/eva/.../19K-RGP.IRGSP-1.0.snps.vcf.gz
    tabix -p vcf 19K-RGP.IRGSP-1.0.snps.vcf.gz

    # Fetch raw reads for one run
    prefetch SRR24065674 && fasterq-dump SRR24065674

## Access & cite

Public Open, anonymous archive access (some records are embargoed during peer review and released at publication).

Cite the manuscript and the relevant archive accession (see Cite & about).