sequana-hic 0.1.0

Hi-C analysis, snakemake, sequana, container, reproducibility

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

Overview:

Hi-C pipeline to capture 3D chromatin interactions in a genome

Input:

Paired FastQ files and a reference genome in FASTA format

Output:

Cooler contact matrices, Hi-C QC reports, and a MultiQC summary

Status:

Beta

Citation:

Cokelaer et al, (2017), ‘Sequana’: a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI https://doi:10.21105/joss.00352

Installation

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.

Usage

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.).

Usage with apptainer

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"

Requirements

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)

Pipeline description

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

Changelog

Version	Description
0.1.0	Migration to modern sequana_pipetools framework (get_shell/get_run, schema validation, apptainer support, Python 3.10+).
0.0.1	First release.

Contribute & Code of Conduct

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.