Pre-built Subread Genome Index (Human GRCh38)

Get straight to read alignment with Subread. This repository provides a shell script to instantly download (high-speed CDN) and deploy a pre-built Subread index for the human genome, skipping the genome download and subread-buildindex step, going from ~81 minutes to ~3 minutes (~27x faster) before you're ready to run subread-align or subjunc. Especially useful for synchronous bioinformatics workshops (no one stuck waiting or falling behind), or simply to save time and skip transferring large genome files between machines.

Index Specifications

• Organism: Homo sapiens (Human)
• Assembly: GRCh38 / hg38 (Primary Assembly)
• Source: Ensembl GRCh38 Release DNA Primary Assembly
• Parameters: Subread defaults (indexSplit=TRUE for 8GB RAM footprint compatibility)
• Archive Size: ~4.7 GB (Highly compressed)
• Estimated Download Time: ~2-3 minutes (via Pixeldrain high-speed CDN, depending on your connection)
• SHA256 Checksum: f9d90ba5dd7c207455bd80e752ce9c2c06a6f9faa0a1e7270c8742b8eb3d1b4d

Quick Start

You can download the index automatically using our helper script or do it step-by-step manually.

Option A: Automated Setup (Recommended)

Clone this repository and run the setup script to download and extract the index automatically:

git clone https://github.com/epilabco/human-grch38-subread-index.git
cd human-grch38-subread-index
bash download_index.sh

Note: after the script finishes, it moves the extracted subread-index/ folder one level up and deletes the cloned repo folder, so you're left with a clean ./subread-index/ directory (no repo files) in the location where you ran git clone.

Option B: Manual Setup

If you prefer to handle it manually:

# 1. Download the 4.7GB index from Pixeldrain
wget https://pixeldrain.com/u/d2WwvJGs -O subread-index-grch38.tar.gz

# 2. (Optional but recommended) Verify the archive's integrity
echo "f9d90ba5dd7c207455bd80e752ce9c2c06a6f9faa0a1e7270c8742b8eb3d1b4d  subread-index-grch38.tar.gz" | sha256sum -c -

# 3. Extract the files (use pigz piped into tar if you have it installed, it's faster)
pigz -dc subread-index-grch38.tar.gz | tar -xvf -
# or, without pigz:
# tar -xzvf subread-index-grch38.tar.gz

# 4. Run your alignment using the index prefix
subread-align -i ./subread-index/grch38-index -r reads_1.fastq -R reads_2.fastq -o aligned_output.bam