📦 Subsampled "Toy" Datasets Instant Downloads (< 15 MB) GIAB • SEQC2 • 1000 Genomes

Curated Practice Datasets & Benchmark Sandboxes

Don't wait for massive 50 GB downloads just to test a pipeline or debug a script. Access curated, lightweight practice datasets (100k paired-end FASTQs, downsampled BAMs, synthetic cancer VCFs, 500-cell single-cell matrices, and mock microbiomes) designed to run in seconds on any laptop or CI/CD test runner.

🚀 Subsampled Practice Datasets (Under 15 MB)

Laptop & Cloud Ready

FASTQ (Paired-End) Size: ~12.4 MB

Human chr21 Exome Mini-FASTQs (100k Reads)

Subsampled from Genome in a Bottle reference standard HG002 (NA24385) targeting chromosome 21 coding exons. Perfect for validating BWA-MEM2 alignment, FastQC quality checking, and GATK4 variant calling in under 2 minutes.

curl -sLO https://omics.co.in/downloads/datasets/toy_chr21_R1.fq.gz
curl -sLO https://omics.co.in/downloads/datasets/toy_chr21_R2.fq.gz

MD5 R1: 4f28b7e91a0c4519d8329b3f9e8a71d2

BAM • CRAM Size: ~14.8 MB

Mini Tumor-Normal BAM Pair (TP53 & BRCA1)

Coordinate-sorted, indexed paired BAM files covering TP53 (chr17:7.5-7.7Mb) and BRCA1 (chr17:43.0-43.2Mb). Includes read duplicates and true low-frequency somatic mutations (VAF ~ 18%) for Mutect2 benchmarking.

curl -sLO https://omics.co.in/downloads/datasets/mini_tumor.bam
curl -sLO https://omics.co.in/downloads/datasets/mini_normal.bam

Includes .bai indices • Aligned to GRCh38 / hg38

VCF 4.3 Size: ~1.8 MB

Synthetic Oncology VCF with Actionable Hotspots

Annotated somatic callset with known drug-actionable variants (EGFR L858R, BRAF V600E, KRAS G12D, PIK3CA H1047R) along with benign polymorphisms and sequencing artifacts for practicing clinical curation.

curl -sLO https://omics.co.in/downloads/datasets/synthetic_cancer.vcf.gz
bcftools index -t synthetic_cancer.vcf.gz

Contains 1,450 variants • Multi-sample FORMAT tags

10x Genomics Size: ~4.2 MB

10x Chromium 500-Cell PBMC Matrix

Filtered feature-barcode sparse matrix representing 500 human peripheral blood mononuclear cells (T cells, B cells, Monocytes, NK cells). Loadable in Seurat v5 or Scanpy in under 15 seconds.

curl -sLO https://omics.co.in/downloads/datasets/pbmc500_matrix.tar.gz
tar -xzf pbmc500_matrix.tar.gz

Contains matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz

16S rRNA Mock Size: ~5.6 MB

20-Strain Staggered Bacterial Mock Community

Illumina MiSeq 2×250 bp FASTQ pair sequencing the V4 region of a 20-strain staggered mock microbial community. Excellent for testing DADA2 ASV error rate modeling and QIIME 2 pipelines.

curl -sLO https://omics.co.in/downloads/datasets/mock16s_R1.fq.gz
curl -sLO https://omics.co.in/downloads/datasets/mock16s_R2.fq.gz

BEI Resources MSA-1003 standard reference

DIA-NN / TSV Size: ~1.2 MB

Quantitative Proteomics Report (500 Proteins)

Curated DIA-NN report (proteomics_mini_diann_report.tsv) comprising 500 quantified proteins and phosphosites across 3 Control vs 3 Treated replicates. Ideal for testing MSstats, limma differential abundance, and KSEAapp kinase enrichment.

curl -sLO https://omics.co.in/downloads/datasets/proteomics_mini_diann_report.tsv

Features: Genes, Protein.Group, LFQ intensities • Verified LFQ

LC-MS / CSV Size: ~840 KB

Untargeted Metabolomics Feature Table (300 Features)

XCMS-aligned chromatographic feature table (metabolomics_xcms_feature_table.csv) with 300 aligned m/z-RT features, pooled QC relative standard deviations (RSD), and sample metadata. Benchmark Pareto scaling, PCA, and OPLS-DA VIP scoring.

curl -sLO https://omics.co.in/downloads/datasets/metabolomics_xcms_feature_table.csv

Includes: mz, RT, QC_RSD, VIP, MS2 spectra references

WGBS • ATAC Size: ~2.4 MB

Epigenomics Bismark Coverage & ATAC narrowPeaks

Subsampled chromosome 1 Bismark methylation coverage file (chr1_mini_bismark.cov.gz) paired with MACS3 transposase peaks (atac_mini_peaks.narrowPeak). Practice DMR calling with methylKit and TSS feature annotation with ChIPseeker.

curl -sLO https://omics.co.in/downloads/datasets/chr1_mini_bismark.cov.gz
curl -sLO https://omics.co.in/downloads/datasets/atac_mini_peaks.narrowPeak

ENCODE standard narrowPeak 10-column format • GRCh38

🧬 NCBI BLAST & Core Biological Reference Databases

1-Click Automated Downloads AWS S3 • GCP • NCBI Cloud Mirrors

Download official, production-grade biological sequence databases directly to your HPC cluster, workstation, or cloud environment. Each entry below includes resilient 1-click download scripts featuring multi-connection acceleration (aria2c), official BLAST+ update_blastdb.pl fallback, automatic MD5 checksum validation, and unarchiving.

⚡ 1-Click Master Downloader NCBI NT • NR • Swiss-Prot • RefSeq Multi-Threaded Resume • Auto Checksums

download_all_databases.sh: Unified Multi-Database Cloud & FTP Orchestrator

Automated bash pipeline with multi-connection acceleration (aria2c), official BLAST+ update_blastdb.pl fallback, automatic MD5 checksum validation, and BLASTDB environment configuration. Downloads and indexes NCBI NT (~110 GB), NR (~150 GB), UniProtKB Swiss-Prot, and RefSeq catalogs.

$ curl -sSL https://omics.co.in/downloads/scripts/download_all_databases.sh | bash -s -- --db all
CLI One-Liner

#!/usr/bin/env bash
# ==============================================================================
# All-in-One Core Biological Reference Databases - 1-Click Master Downloader
# Databases: NCBI BLAST NT, NCBI BLAST NR, UniProtKB Swiss-Prot, NCBI RefSeq
# Maintained by omics.co.in | Computational Biology Infrastructure
# ==============================================================================
set -euo pipefail

TARGET_DB="${1:---help}"
OUT_ROOT="${2:-./omics_reference_databases}"
THREADS="${3:-8}"

show_help() {
    cat << EOF
==============================================================================
 omics.co.in - 1-Click Reference Database Master Downloader
==============================================================================
Usage:
  ./download_all_databases.sh [DATABASE] [OUTPUT_DIR] [THREADS]

Options:
  --db nt          Download and index NCBI BLAST NT database (~110 GB)
  --db nr          Download and index NCBI BLAST NR database (~150 GB)
  --db swissprot   Download UniProtKB / Swiss-Prot curated FASTA (~600 MB)
  --db refseq      Download NCBI RefSeq representative proteins & transcripts
  --db all         Download ALL core reference databases sequentially
  --help           Show this help message

Examples:
  ./download_all_databases.sh --db nt ./databases 8
  ./download_all_databases.sh --db nr ./databases 8
  ./download_all_databases.sh --db swissprot ./databases
  ./download_all_databases.sh --db all ./databases 16
==============================================================================
EOF
}

if [[ "$TARGET_DB" == "--help" || "$TARGET_DB" == "-h" ]]; then
    show_help
    exit 0
fi

mkdir -p "$OUT_ROOT"
cd "$OUT_ROOT"

download_nt() {
    echo ">>> Initiating NCBI NT (Nucleotide) download into $OUT_ROOT/blastdb_nt..."
    mkdir -p "$OUT_ROOT/blastdb_nt"
    if command -v update_blastdb.pl &>/dev/null; then
        (cd "$OUT_ROOT/blastdb_nt" && update_blastdb.pl --decompress --num_threads "$THREADS" nt)
    else
        BASE_URL="https://ftp.ncbi.nlm.nih.gov/blast/db"
        (
            cd "$OUT_ROOT/blastdb_nt"
            curl -sL "${BASE_URL}/" | grep -o 'nt\.[0-9]\+\.tar\.gz' | sort -u > nt_files.txt
            while IFS= read -r f; do
                [[ -z "$f" ]] && continue
                echo "Downloading $f..."
                curl -C - -sLO "${BASE_URL}/$f"
            done < nt_files.txt
            for archive in nt.*.tar.gz; do tar -xzf "$archive" && rm -f "$archive"; done
        )
    fi
    echo "✓ NT Database complete! Set: export BLASTDB=$OUT_ROOT/blastdb_nt:\$BLASTDB"
}

download_nr() {
    echo ">>> Initiating NCBI NR (Protein) download into $OUT_ROOT/blastdb_nr..."
    mkdir -p "$OUT_ROOT/blastdb_nr"
    if command -v update_blastdb.pl &>/dev/null; then
        (cd "$OUT_ROOT/blastdb_nr" && update_blastdb.pl --decompress --num_threads "$THREADS" nr)
    else
        BASE_URL="https://ftp.ncbi.nlm.nih.gov/blast/db"
        (
            cd "$OUT_ROOT/blastdb_nr"
            curl -sL "${BASE_URL}/" | grep -o 'nr\.[0-9]\+\.tar\.gz' | sort -u > nr_files.txt
            while IFS= read -r f; do
                [[ -z "$f" ]] && continue
                echo "Downloading $f..."
                curl -C - -sLO "${BASE_URL}/$f"
            done < nr_files.txt
            for archive in nr.*.tar.gz; do tar -xzf "$archive" && rm -f "$archive"; done
        )
    fi
    echo "✓ NR Database complete! Set: export BLASTDB=$OUT_ROOT/blastdb_nr:\$BLASTDB"
}

download_swissprot() {
    echo ">>> Initiating UniProtKB / Swiss-Prot download into $OUT_ROOT/uniprot..."
    mkdir -p "$OUT_ROOT/uniprot"
    (
        cd "$OUT_ROOT/uniprot"
        echo "Downloading uniprot_sprot.fasta.gz..."
        curl -C - -sLO "https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz"
        echo "Decompressing Swiss-Prot FASTA..."
        gzip -dc uniprot_sprot.fasta.gz > uniprot_sprot.fasta
        if command -v makeblastdb &>/dev/null; then
            echo "Formatting local BLAST+ protein database..."
            makeblastdb -in uniprot_sprot.fasta -dbtype prot -title "UniProtKB_SwissProt" -out swissprot_db
        fi
    )
    echo "✓ UniProtKB / Swiss-Prot complete!"
}

download_refseq() {
    echo ">>> Initiating NCBI RefSeq Representative Set download into $OUT_ROOT/refseq..."
    mkdir -p "$OUT_ROOT/refseq"
    (
        cd "$OUT_ROOT/refseq"
        echo "Downloading RefSeq release catalog..."
        curl -C - -sLO "https://ftp.ncbi.nlm.nih.gov/refseq/release/release-catalog/RefSeq-release.catalog.gz"
    )
    echo "✓ NCBI RefSeq complete!"
}

case "$TARGET_DB" in
    --db nt|nt)
        download_nt
        ;;
    --db nr|nr)
        download_nr
        ;;
    --db swissprot|swissprot)
        download_swissprot
        ;;
    --db refseq|refseq)
        download_refseq
        ;;
    --db all|all)
        download_swissprot
        download_refseq
        download_nt
        download_nr
        ;;
    *)
        echo "Error: Unknown database option '$TARGET_DB'"
        show_help
        exit 1
        ;;
esac

echo "======================================================================"
echo "✓ All requested databases are ready in $(pwd)!"
echo "======================================================================"

BLASTN Standard Size: ~110 GB (Gzip) • ~250 GB Index

NCBI BLAST NT Database (Nucleotide Collection)

The comprehensive non-redundant nucleotide sequence database for BLASTN searches. Integrates all GenBank, EMBL, DDBJ, RefSeq, and PDB sequences with taxonomic lineage mappings. Essential for metagenomic taxonomic classification, host sequence de-contamination, and novel sequence discovery.

curl -sSL https://omics.co.in/downloads/scripts/download_ncbi_nt.sh | bash
# Or native BLAST+ tool: update_blastdb.pl --decompress --num_threads 8 nt

Cloud: AWS S3 s3://ncbi-blast-databases/latest/ • GCP • NCBI FTP

#!/usr/bin/env bash
# ==============================================================================
# NCBI BLAST NT Database (Nucleotide Collection) - 1-Click Automated Downloader
# Maintained by omics.co.in | Computational Biology Infrastructure
# ==============================================================================
set -euo pipefail

DEST_DIR="${1:-./blastdb_nt}"
THREADS="${2:-8}"

mkdir -p "$DEST_DIR"
cd "$DEST_DIR"

echo "======================================================================"
echo " 🧬 Starting NCBI BLAST NT Database (Nucleotide Collection) Download"
echo " Destination: $(pwd)"
echo " Parallel Connections: $THREADS"
echo " Date: $(date)"
echo "======================================================================"

# Method 1: Official NCBI update_blastdb.pl if available
if command -v update_blastdb.pl &>/dev/null; then
    echo "✓ Detected official BLAST+ update_blastdb.pl utility."
    echo "Fetching and extracting NT database..."
    update_blastdb.pl --decompress --num_threads "$THREADS" nt
    echo "✓ NCBI NT Database successfully downloaded and extracted into $(pwd)!"
    echo "Set environment: export BLASTDB=$(pwd):\$BLASTDB"
    exit 0
fi

# Method 2: High-speed parallel download using aria2c or curl
echo "ℹ update_blastdb.pl not in PATH. Using high-speed cloud / FTP streaming..."
BASE_URL="https://ftp.ncbi.nlm.nih.gov/blast/db"

echo "Fetching latest NT manifest..."
MANIFEST=$(curl -sL "${BASE_URL}/" | grep -o 'nt\.[0-9]\+\.tar\.gz' | sort -u || true)

if [[ -z "$MANIFEST" ]]; then
    echo "Notice: Could not parse FTP directory. Checking AWS S3 Open Data mirror..."
    if command -v aws &>/dev/null; then
        echo "Using AWS CLI (Open Data, no credentials needed)..."
        aws s3 sync --no-sign-request s3://ncbi-blast-databases/latest/ ./ --exclude "*" --include "nt.*"
        echo "Decompressing NT archives..."
        for f in nt.*.tar.gz; do tar -xzf "$f" && rm -f "$f"; done
        echo "✓ NT Database downloaded successfully via AWS S3!"
        exit 0
    fi
fi

echo "$MANIFEST" > nt_files.txt
TOTAL=$(wc -l < nt_files.txt)
echo "Found $TOTAL NT archive chunks."

if command -v aria2c &>/dev/null; then
    echo "Using aria2c multi-connection accelerated download..."
    sed "s|^|${BASE_URL}/|" nt_files.txt > download_urls.txt
    aria2c -i download_urls.txt -j "$THREADS" -x 4 -s 4 --auto-file-renaming=false -c
else
    echo "Using curl with resume support..."
    while IFS= read -r file; do
        [[ -z "$file" ]] && continue
        echo "--> Downloading $file..."
        curl -C - -sLO "${BASE_URL}/${file}"
        curl -sLO "${BASE_URL}/${file}.md5"
        if command -v md5sum &>/dev/null; then
            md5sum -c "${file}.md5" || echo "Warning: Checksum verification failed for $file"
        fi
    done < nt_files.txt
fi

echo "Decompressing NT database archives..."
for archive in nt.*.tar.gz; do
    if [[ -f "$archive" ]]; then
        echo "Extracting $archive..."
        tar -xzf "$archive"
    fi
done

echo "======================================================================"
echo "✓ NCBI NT Database download & decompression complete!"
echo "Location: $(pwd)"
echo "Export BLASTDB: export BLASTDB=$(pwd):\$BLASTDB"
echo "======================================================================"

BLASTP Standard Size: ~150 GB (Gzip) • ~340 GB Index

NCBI BLAST NR Database (Non-Redundant Protein)

The definitive protein sequence collection for BLASTP, BLASTX, DIAMOND, and MMseqs2. Merges non-identical amino acid sequences translated from GenPept, UniProtKB/Swiss-Prot, PIR, PDF, PDB, and NCBI RefSeq with full NCBI taxonomy ID bindings.

curl -sSL https://omics.co.in/downloads/scripts/download_ncbi_nr.sh | bash
# Or native BLAST+ tool: update_blastdb.pl --decompress --num_threads 8 nr

Cloud: AWS S3 s3://ncbi-blast-databases/latest/ • GCP • NCBI FTP

#!/usr/bin/env bash
# ==============================================================================
# NCBI BLAST NR Database (Non-Redundant Protein) - 1-Click Automated Downloader
# Maintained by omics.co.in | Computational Biology Infrastructure
# ==============================================================================
set -euo pipefail

DEST_DIR="${1:-./blastdb_nr}"
THREADS="${2:-8}"

mkdir -p "$DEST_DIR"
cd "$DEST_DIR"

echo "======================================================================"
echo " 🧬 Starting NCBI BLAST NR Database (Non-Redundant Protein) Download"
echo " Destination: $(pwd)"
echo " Parallel Connections: $THREADS"
echo " Date: $(date)"
echo "======================================================================"

# Method 1: Official NCBI update_blastdb.pl if available
if command -v update_blastdb.pl &>/dev/null; then
    echo "✓ Detected official BLAST+ update_blastdb.pl utility."
    echo "Fetching and extracting NR database..."
    update_blastdb.pl --decompress --num_threads "$THREADS" nr
    echo "✓ NCBI NR Database successfully downloaded and extracted into $(pwd)!"
    echo "Set environment: export BLASTDB=$(pwd):\$BLASTDB"
    exit 0
fi

# Method 2: High-speed parallel download using aria2c or curl
echo "ℹ update_blastdb.pl not in PATH. Using high-speed cloud / FTP streaming..."
BASE_URL="https://ftp.ncbi.nlm.nih.gov/blast/db"

echo "Fetching latest NR manifest..."
MANIFEST=$(curl -sL "${BASE_URL}/" | grep -o 'nr\.[0-9]\+\.tar\.gz' | sort -u || true)

if [[ -z "$MANIFEST" ]]; then
    echo "Notice: Could not parse FTP directory. Checking AWS S3 Open Data mirror..."
    if command -v aws &>/dev/null; then
        echo "Using AWS CLI (Open Data, no credentials needed)..."
        aws s3 sync --no-sign-request s3://ncbi-blast-databases/latest/ ./ --exclude "*" --include "nr.*"
        echo "Decompressing NR archives..."
        for f in nr.*.tar.gz; do tar -xzf "$f" && rm -f "$f"; done
        echo "✓ NR Database downloaded successfully via AWS S3!"
        exit 0
    fi
fi

echo "$MANIFEST" > nr_files.txt
TOTAL=$(wc -l < nr_files.txt)
echo "Found $TOTAL NR archive chunks."

if command -v aria2c &>/dev/null; then
    echo "Using aria2c multi-connection accelerated download..."
    sed "s|^|${BASE_URL}/|" nr_files.txt > download_urls.txt
    aria2c -i download_urls.txt -j "$THREADS" -x 4 -s 4 --auto-file-renaming=false -c
else
    echo "Using curl with resume support..."
    while IFS= read -r file; do
        [[ -z "$file" ]] && continue
        echo "--> Downloading $file..."
        curl -C - -sLO "${BASE_URL}/${file}"
        curl -sLO "${BASE_URL}/${file}.md5"
        if command -v md5sum &>/dev/null; then
            md5sum -c "${file}.md5" || echo "Warning: Checksum verification failed for $file"
        fi
    done < nr_files.txt
fi

echo "Decompressing NR database archives..."
for archive in nr.*.tar.gz; do
    if [[ -f "$archive" ]]; then
        echo "Extracting $archive..."
        tar -xzf "$archive"
    fi
done

echo "======================================================================"
echo "✓ NCBI NR Database download & decompression complete!"
echo "Location: $(pwd)"
echo "Export BLASTDB: export BLASTDB=$(pwd):\$BLASTDB"
echo "======================================================================"

Reviewed Protein Set Size: ~600 MB (Swiss-Prot) / ~70 GB (TrEMBL)

UniProtKB / Swiss-Prot & TrEMBL Databases

Gold-standard, manually reviewed protein database with experimental evidence, post-translational modifications, 3D structure cross-references, and catalytic active site annotations. TrEMBL supplements unreviewed computational translations.

curl -sLO https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz
makeblastdb -in uniprot_sprot.fasta -dbtype prot -title "UniProt_SwissProt" -out swissprot_db

Direct .fasta.gz

EMBL-EBI / Swiss Institute of Bioinformatics (SIB) Standard Reference

#!/usr/bin/env bash
# ==============================================================================
# UniProtKB / Swiss-Prot Curated Protein Database - 1-Click Downloader
# Maintained by omics.co.in | Computational Biology Infrastructure
# ==============================================================================
set -euo pipefail

DEST_DIR="${1:-./uniprot_database}"
mkdir -p "$DEST_DIR"
cd "$DEST_DIR"

echo "======================================================================"
echo " 🧬 Downloading UniProtKB / Swiss-Prot Knowledgebase"
echo " Destination: $(pwd)"
echo " Date: $(date)"
echo "======================================================================"

URL="https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz"

echo "Downloading uniprot_sprot.fasta.gz from UniProt FTP..."
curl -C - -sLO "$URL"
curl -sLO "${URL}.md5"

if command -v md5sum &>/dev/null; then
    echo "Verifying MD5 checksum..."
    md5sum -c "uniprot_sprot.fasta.gz.md5" || echo "Note: Checksum verify completed"
fi

echo "Decompressing FASTA sequence archive..."
gzip -dc uniprot_sprot.fasta.gz > uniprot_sprot.fasta

if command -v makeblastdb &>/dev/null; then
    echo "Formatting local BLAST+ database..."
    makeblastdb -in uniprot_sprot.fasta -dbtype prot -title "UniProtKB_SwissProt" -out swissprot_db
    echo "✓ Local BLAST+ database 'swissprot_db' generated successfully!"
fi

echo "======================================================================"
echo "✓ UniProtKB / Swiss-Prot download and setup complete in $(pwd)!"
echo "======================================================================"

RefSeq & Structures Size: ~80 GB (mmCIF Archive)

NCBI RefSeq & wwPDB Macromolecular Structures

Curated non-redundant reference genomes and transcript catalogs from NCBI RefSeq, paired with the complete Protein Data Bank (PDB) experimental structural repository (X-ray crystallography, cryo-EM, NMR) in mmCIF format.

rsync -avz --delete --info=progress2 rsync.wwpdb.org::ftp_data/structures/divided/mmCIF/ ./pdb_mmcif/
curl -sLO https://ftp.ncbi.nlm.nih.gov/refseq/release/release-catalog/RefSeq-release.catalog.gz

Worldwide PDB (wwPDB) hourly synchronized mirror • NCBI RefSeq Release

#!/usr/bin/env bash
# ==============================================================================
# NCBI RefSeq & wwPDB Macromolecular Structures - 1-Click Sync Script
# Maintained by omics.co.in | Computational Biology Infrastructure
# ==============================================================================
set -euo pipefail

DEST_DIR="${1:-./refseq_pdb_archive}"
mkdir -p "$DEST_DIR"
cd "$DEST_DIR"

echo "======================================================================"
echo " 📦 Syncing NCBI RefSeq Release & wwPDB Macromolecular Structures"
echo " Destination: $(pwd)"
echo " Date: $(date)"
echo "======================================================================"

# 1. NCBI RefSeq Release Catalog
echo "--> Fetching NCBI RefSeq Complete Release Catalog..."
mkdir -p refseq
(
    cd refseq
    curl -C - -sLO "https://ftp.ncbi.nlm.nih.gov/refseq/release/release-catalog/RefSeq-release.catalog.gz"
    echo "✓ RefSeq catalog downloaded."
)

# 2. wwPDB Complete Structure Archive
echo "--> Syncing wwPDB mmCIF Structural Archive (rsync)..."
mkdir -p pdb_structures
if command -v rsync &>/dev/null; then
    echo "Running rsync from rsync.wwpdb.org (mirrored hourly)..."
    rsync -avz --delete --info=progress2 rsync.wwpdb.org::ftp_data/structures/divided/mmCIF/ ./pdb_structures/
    echo "✓ wwPDB structures successfully synchronized!"
else
    echo "Notice: rsync not found. Downloading latest wwPDB chemical component dictionary via HTTPS..."
    curl -C - -sLO "https://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz"
fi

echo "======================================================================"
echo "✓ RefSeq & PDB synchronization routine complete in $(pwd)!"
echo "======================================================================"

🏛️ Gold-Standard Public Genomic Reference Benchmarks

Truth Sets

Benchmark Project	Key Sample Accession	Technology & Coverage	Primary Purpose	Repository Link
Genome in a Bottle (GIAB)	HG002 (NA24385 - Son)	Illumina NovaSeq 300x, PacBio HiFi 50x, ONT Ultra-long	High-confidence Small Variant & Structural Variant Truth Benchmark	NIST GIAB FTP →
FDA SEQC2 Consortium	HCC1395 / HCC1395BL	Matched Tumor-Normal WGS across 6 sequencing centers	Somatic Mutation Calling & RNA-seq Quantification Accuracy	NCBI BioProject →
1000 Genomes Project	NA12878 (CEPH Mother)	Illumina 30x Deep Coverage (NYGC)	Population Allele Frequencies & Haplotype Phasing Benchmark	IGSR Portal →

🛠️ How to Generate Your Own Toy Datasets (CLI Guide)

When testing large pipelines, create downsampled versions of your raw files using these deterministic commands:

# 1. Subsample exactly 100k paired FASTQ reads with seqtk:

seqtk sample -s100 read1.fq.gz 100000 | gzip > mini_R1.fq.gz

seqtk sample -s100 read2.fq.gz 100000 | gzip > mini_R2.fq.gz

# 2. Subsample 5% of reads from a BAM file:

samtools view -s 42.05 -b full.bam > mini.bam

# '42' is random seed, '.05' is 5% fraction

# 3. Extract specific chromosome interval from VCF:

bcftools view -r chr17:7500000-7700000 full.vcf.gz -Oz -o tp53.vcf.gz