Public Resources

This page lists reference resources commonly used with SpaceTracer.

Recommended for first-time users to avoid manual reference setup.

  • Source: Zenodo resource package (SpaceTracer v2.1.0)
  • Main archive: resources.tar.tar (~11.5 GB)
  • Demo archive: demo.zip (~4.4 MB)
  • Includes:
  • mm10_resources.tar.zst (mouse, mm10 / GRCm38)
  • hg38_resources.tar.zst (human, hg38 / GRCh38)

Download from Zenodo with wget (append ?download=1 so the server serves the file directly):

# Full reference package (~11.5 GB) — pick a working directory first
wget -O resources.tar "https://zenodo.org/records/19896967/files/resources.tar.tar?download=1"

# Optional: small demo package from the same record
wget -O demo.zip "https://zenodo.org/records/19896967/files/demo.zip?download=1"

If you prefer curl, use:

curl -L -o resources.tar "https://zenodo.org/records/19896967/files/resources.tar.tar?download=1"

Extract references:

tar -xf resources.tar

# mm10
mkdir -p mm10
zstd -dc mm10_resources.tar.zst | tar -xf - -C mm10

# hg38
mkdir -p hg38
zstd -dc hg38_resources.tar.zst | tar -xf - -C hg38

Extract the demo package:

unzip demo.zip

The demo package contains human_visium_demo_input.tar and human_visium_demo_output.tar. See Demo for extraction, config editing, and run instructions.

If you need custom references, use the resource links below to build your own.

Human reference genome example

GRCh37 / hg19

wget ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz
wget ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz.fai

GRCh38 / hg38

wget ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/GRCh38_reference_genome/GRCh38_full_analysis_set_plus_decoy_hla.fa
wget ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/GRCh38_reference_genome/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai

NCBI reference page: NCBI human datasets.

Annotation and supporting resources