This is the Hi-C pipeline from the Sequana project.

If you already have all requirements, install the package with pip:

pip install sequana_hic --upgrade

You will need third-party tools (see Requirements below). Use apptainer images to avoid installing them locally.

Set up the pipeline directory with your input data and reference:

sequana_hic --input-directory DATAPATH --reference-file genome.fa
sequana_hic --input-directory DATAPATH --reference-file genome.fa --aligner-choice bwa_split

This creates a hic/ directory containing the pipeline and configuration file. Execute the pipeline locally:

cd hic
sh hic.sh

See .sequana/profile/config.yaml to tune Snakemake behaviour (cores, cluster settings, etc.).

With Apptainer, initiate the working directory as follows:

sequana_hic --input-directory DATAPATH --reference-file genome.fa --use-apptainer

Images can be stored in a shared location:

sequana_hic --input-directory DATAPATH --reference-file genome.fa --use-apptainer --apptainer-prefix ~/.sequana/apptainers

then:

cd hic
sh hic.sh

If running Snakemake manually, add apptainer options:

snakemake -s hic.rules --cores 4 --use-apptainer --apptainer-prefix ~/.sequana/apptainers --apptainer-args "-B /home:/home"

By default the home directory is already bound. Additional paths can be set via:

export APPTAINER_BINDPATH="-B /pasteur"

This pipeline requires the following executables (install via bioconda/conda):

• bwa — short-read aligner (default mapper)
• samtools — BAM/SAM manipulation
• pairtools — processing of Hi-C read pairs
• cooler — storage and analysis of Hi-C contact matrices
• qc3c — Hi-C quality control
• fastqc — raw read quality control
• multiqc — aggregate QC reports

Optional:

• chromap — fast Hi-C aligner (experimental, use --aligner-choice chromap)
• seqkit — split FastQ files (required for --aligner-choice bwa_split)

1. FastQC — quality control on raw reads
2. Reference indexing — BWA index build from the provided FASTA reference
3. Alignment — BWA-MEM alignment with Hi-C-specific options (-5SP), producing sorted BAM files
4. Pairtools — parse alignments into Hi-C contact pairs, sort, deduplicate, and split
5. Cooler — load pairs into a contact matrix and generate multi-resolution .mcool file
6. qc3C — Hi-C library quality assessment (ligation efficiency, distance distribution)
7. Visualisation — contact matrix PNG at 5 kb resolution
8. MultiQC — aggregated QC report

To contribute to this project, please take a look at the Contributing Guidelines first. Please note that this project is released with a Code of Conduct. By contributing to this project, you agree to abide by its terms.