Kleboscope is a comprehensive bioinformatics pipeline for complete genomic characterization of Klebsiella pneumoniae. It integrates seven core analysis modules into a single automated workflow:
Perfect for clinical microbiology, outbreak investigations, and genomic surveillance.
📖 Full documentation, examples, and Conda installation instructions are available on the GitHub repository:
👉 https://github.com/bbeckley-hub/Kleboscope
abricate --setupdb already run)docker pull bbeckleyhub/kleboscope:latest
docker run --rm -v $(pwd):/data bbeckleyhub/kleboscope:latest -i "/data/genome.fna" -o /data/output
After the run, output files are owned by root on your host. To reclaim ownership:
sudo chown -R $USER:$USER ./output
docker run --rm -v $(pwd):/data bbeckleyhub/kleboscope:latest -i "/data/*.fna" -o /data/output
docker run --rm -v $(pwd):/data bbeckleyhub/kleboscope:latest [OPTIONS]
--rm : remove container after exit-v $(pwd):/data : mount current directory to /data inside container/data (e.g., /data/*.fna)/data (e.g., /data/output)docker run --rm -v $(pwd):/data bbeckleyhub/kleboscope:latest \
-i "/data/*.fna" -o /data/output \
--threads 8 --skip-qc --skip-amr
See docker run --rm bbeckleyhub/kleboscope:latest -h for all options.
docker run --rm -v $(pwd):/data bbeckleyhub/kleboscope:latest \
-i "/data/*.fna" -o /data/output -t 16
By default, Docker runs as root inside the container. Any files written to your mounted directory will be owned by root:root.
You have three options:
sudo chown -R $USER:$USER ./output
Currently not fully supported because Kleboscope needs to write to its own installation directory. A future update will fix this.
sudo needed)See the Singularity section below.
docker run --rm bbeckleyhub/kleboscope:latest -h
docker run --rm --entrypoint /bin/bash bbeckleyhub/kleboscope:latest -c "abricate --list | head -5"
Expected output: list of databases (ncbi, card, vfdb, etc.)
docker run --rm --entrypoint /bin/bash bbeckleyhub/kleboscope:latest -c "jq --version"
Should output jq-1.6 or similar.
sudo, correct ownership)On HPC clusters that support Singularity/Apptainer, you can run Kleboscope without sudo and output files will be owned by your user automatically.
Important: Kleboscope writes temporary files inside its own installation directory (e.g.,
/opt/kleboscope/...). Singularity mounts containers as read‑only by default, so you must add the--writable-tmpfsflag to allow these writes. The flag creates an ephemeral, writable overlay in memory – no permanent changes are made to the container.
singularity pull kleboscope.sif docker://bbeckleyhub/kleboscope:latest
singularity run --writable-tmpfs -B $(pwd):/data kleboscope.sif -i "/data/*.fna" -o /data/output
singularity pull fails)If you encounter TLS timeouts or other network errors (common on some HPCs), convert an existing Docker image to a Singularity SIF file on a machine with Docker, then transfer the .sif file to the HPC.
Step 1 – on a machine with Docker (e.g., your laptop):
docker pull bbeckleyhub/kleboscope:latest
docker save bbeckleyhub/kleboscope:latest -o kleboscope.tar
singularity build kleboscope.sif docker-archive://kleboscope.tar
Now copy kleboscope.sif to your HPC home or project directory (e.g., using scp).
Step 2 – on the HPC (no sudo needed):
singularity run --writable-tmpfs -B $(pwd):/data kleboscope.sif -i "/data/*.fna" -o /data/output
| Flag | Purpose |
|---|---|
--writable-tmpfs | Creates a temporary writable overlay – required for Kleboscope to write intermediate files to /opt/... |
-B $(pwd):/data | Binds your current directory to /data inside the container (input files are read from here, output is written here) |
-i "/data/*.fna" | Input pattern – use quotes to prevent shell expansion on the host |
-o /data/output | Output directory (will appear as ./output on your host) |
You can use any Kleboscope flag, e.g.:
singularity run --writable-tmpfs -B $(pwd):/data kleboscope.sif \
-i "/data/*.fna" -o /data/output --threads 8 --skip-qc
After a successful run, you will see output indicating each module completed. All result files in ./output will be owned by your HPC user – no sudo chown needed.
After a successful run, your output directory will contain:
output/
├── fasta_qc_results/ # Quality control reports per sample
├── mlst_results/ # MLST results (Pasteur scheme)
├── kaptive_results/ # Capsule (K) and O locus typing
├── klebo_abricate_results/ # Multi-database screening (11 DBs)
├── klebo_amrfinder_results/ # AMR gene detection with risk levels
└── KLEBOSCOPE_ULTIMATE_REPORTS/ # 🎯 FINAL INTEGRATED REPORT
├── kleboscope_ultimate_report.html # Interactive gene‑centric HTML dashboard
├── kleboscope_ultimate_report.json # Complete data (machine‑readable)
└── *.csv files for easy import into spreadsheets
The main interactive report is KLEBOSCOPE_ULTIMATE_REPORTS/kleboscope_ultimate_report.html.
Docker containers run as root by default. Use sudo chown or Singularity to fix ownership.
--user $(id -u):$(id -g)?Not yet – Kleboscope currently needs to write into its own installation directory. A future update will remove this limitation.
Approximately 1–2 GB (includes Conda, all dependencies, ABRicate databases, and Kaptive).
Yes, with Docker Desktop. Mount paths must be absolute (e.g., -v /c/Users/name/data:/data on Windows Git Bash).
The image is built for linux/amd64. On Apple Silicon, Docker will use emulation (may be slower).
Kleboscope Docker image bundles the same tools as the Conda package. See the main README for third‑party licenses.
If you use Kleboscope in research, please cite:
@software{kleboscope2026,
author = {Beckley Brown et. al},
title = {Kleboscope: A gene‑centric, species‑optimized computational pipeline for comprehensive Klebsiella pneumoniae genomic surveillance},
year = {2026},
url = {https://github.com/bbeckley-hub/Kleboscope}
}
⭐ Star the project on GitHub if it helps your research!
Content type
Image
Digest
sha256:ac594cbf6…
Size
1.4 GB
Last updated
2 months ago
docker pull bbeckleyhub/kleboscope