flobenhsj/expansion_hunter_denovo repository overview

⁠🧬 ExpansionHunterDenovo Docker / Apptainer Image (v0.9.0)

Repository: flobenhsj/expansion_hunter_denovo Upstream project: https://github.com/Illumina/ExpansionHunterDenovo⁠ Tool version: ExpansionHunterDenovo v0.9.0 Image size: ~223 MB Container formats: Docker / Apptainer (SIF supported)

⁠🔬 Overview

This container provides a fully reproducible and HPC-ready environment for running ExpansionHunterDenovo, a tool for reference-free discovery and profiling of short tandem repeat (STR) expansions from short-read sequencing data.

It is particularly suited for:

• genome-wide detection of novel repeat expansions
• large-scale cohort and case-control STR studies
• population-scale WGS analyses

The image is fully preconfigured with ExpansionHunterDenovo v0.9.0 and all required dependencies, ensuring portability across HPC clusters, cloud environments, and local systems without manual installation.

⁠🧠 Key Features

• 🚀 Genome-wide discovery of repeat expansions from BAM/CRAM files
• 🧪 Case-control STR association analysis workflows
• 📦 Prepackaged ExpansionHunterDenovo v0.9.0 environment
• 🧬 Designed for large-scale cohort sequencing studies
• 🖥️ Compatible with Docker and Apptainer (Singularity)
• 🔁 Fully reproducible pipelines for HPC workflows

⁠⚙️ Typical Workflow

⁠1. Per-sample STR profiling

apptainer exec "${SIF}" ExpansionHunterDenovo profile \
    --reads sample.bam \
    --reference reference.fasta \
    --output-prefix sample \
    --min-anchor-mapq 50 \
    --max-irr-mapq 40

⁠2. Merge cohort profiles

apptainer exec "${SIF}" ExpansionHunterDenovo merge \
    --reference reference.fasta \
    --manifest manifest.tsv \
    --output-prefix cohort_output

⁠3. Case-control locus analysis

apptainer exec "${SIF}" /opt/ExpansionHunterDenovo-v0.9.0-linux_x86_64/scripts/casecontrol.py locus \
    --manifest manifest.tsv \
    --multisample-profile cohort_output.multisample_profile.json \
    --output cohort_output.casecontrol_locus.tsv

⁠📊 Inputs

• Aligned sequencing reads (BAM/CRAM)
• Reference genome FASTA
• Cohort manifest file (for multi-sample analyses)

⁠📤 Outputs

• Per-sample STR profiles (JSON)
• Cohort merged STR profiles
• Case-control locus association tables (TSV)
• Downstream-ready files for statistical genetics workflows

⁠🧬 Applications

• Rare disease genomics (e.g. neurodevelopmental disorders)
• Discovery of pathogenic repeat expansions
• Case-control association studies of STR variation
• Population-scale structural variant screening
• Integration into Snakemake / Nextflow pipelines

⁠🧾 Notes

• Built from the official ExpansionHunterDenovo project: https://github.com/Illumina/ExpansionHunterDenovo⁠
• Optimized for reproducible HPC deployment via Apptainer
• Suitable for both exploratory and production-grade genomic workflows