Public Resources

This page lists reference resources commonly used with SpaceTracer.

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

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

# Full reference package (~7 GB) — pick a working directory first
wget -O resources.tar "https://zenodo.org/records/19896967/files/resources.tar?download=1"

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

curl -L -o resources.tar "https://zenodo.org/records/19896967/files/resources.tar?download=1" works the same way if you prefer curl.

Extract references:

tar -xf resources.tar

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

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

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