Asm4pg

Asm4pg is an automatic and reproducible genome assembly workflow designed for pangenomic applications using PacBio HiFi data.

This workflow leverages Snakemake for efficient genome assembly and generates an HTML report summarizing key assembly statistics.

📂 Repository Structure

├── README.md
├── job.sh
├── local_run.sh
├── doc
├── workflow
│   ├── scripts
|   └── Snakefile
└──  .config
    ├── snakemake_profile
    └── masterconfig.yaml

✅ Requirements

• Miniforge (or Snakemake 8.4.7 localy)
• Singularity/Apptainer (for containerized execution)

Note: All external tools are automatically managed by Snakemake and will be downloaded as Singularity/Apptainer images (~6GB total).

🚀 How to Use

1. Set up

Clone the Git repository

git clone https://forgemia.inra.fr/asm4pg/GenomAsm4pg.git && cd GenomAsm4pg

All other tools will be run in Singularity/Apptainer docker images are automatically downloaded and converted by Snakemake. Total size of the images is ~6G

2. Configure the pipeline

• Edit the masterconfig file in the .config/ directory with your sample information.

3. Run the workflow

A. On a HPC (SLURM)

• Update job.sh with the correct paths to Singularity/Apptainer and Miniforge.
• Provide and environment with Snakemake and snakemake-executor-plugin-slurm in job.sh, under source activate wf_env, you can create it like this :

conda create -n wf_env -c conda-forge -c bioconda snakemake=8.4.7 snakemake-executor-plugin-slurm

Use Miniforge with the conda-forge channel, see why here (french)

• Add the log directory for SLURM

mkdir slurm_logs

• Run the workflow :

sbatch job.sh dry # Check for warnings
sbatch job.sh run # Then

Nb 1: If your account name can't be automatically determined, add it in the .config/snakemake/profiles/slurm/config.yaml file.

B. Locally (or single node HPC)

• Make sure you have Snakemake and Singularity/Apptainer installed
• Run the workflow :

./local_run dry # Check for warnings
./local_run job.sh run # Then

🔄 Input Conversion

Currently, asm4pg requires fasta.gz files. To convert your fastq or bam files to this format, you can use the following tools:

./workflow/scripts/input_conversion.sh -i <input_file> -o <output_file>

Nb : Uncomment line 13 and 14 if you are on a HPC and update with your paths

🔧 Using the full potential of the workflow :

Asm4pg has many options. If you wish to modify the default values and know more about the workflow, please refer to the documentation

📜 How to cite asm4pg?

We are currently writing a publication about asm4pg. Meanwhile, if you use the pipeline, please cite it using the address of this repository.

License

The content of this repository is licensed under (GNU GPLv3)

✉️ Contacts

For any troubleshooting, issue or feature suggestion, please use the issue tab of this repository. For any other question or if you want to help in developing asm4pg, please contact Ludovic Duvaux at ludovic.duvaux@inrae.fr