This is the Hi-C pipeline from the Sequana project
| Overview: | Hi-C pipeline to capture 3D chromatim interactions in a genome |
|---|---|
| Input: | FastQ files and reference genome |
| Output: | cooler files and dreamy plots |
| Status: | draft |
| Citation: | Cokelaer et al, (2017), ‘Sequana’: a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI doi:10.21105/joss.00352 |
sequana_hic is based on Python3, just install the package as follows:
pip install sequana_hic --upgrade
You will need third-party software such as fastqc. Please see below for details.
sequana_pipelines_hic --help sequana_pipelines_hic --input-directory DATAPATH
This creates a directory with the pipeline and configuration file. You will then need to execute the pipeline:
cd hic sh hic.sh # for a local run
This launch a snakemake pipeline. If you are familiar with snakemake, you can retrieve the pipeline itself and its configuration files and then execute the pipeline yourself with specific parameters:
snakemake -s hic.rules -c config.yaml --cores 4 --stats stats.txt
Or use sequanix interface.
With Apptainer, initiate the working directory as follows:
sequana_hic --use-apptainer
Images are downloaded in the working directory but you can store then in a directory globally (e.g.):
sequana_hic --use-apptainer --apptainer-prefix ~/.sequana/apptainers
and then:
cd hic sh hic.sh
if you decide to use snakemake manually, do not forget to add apptainer options:
snakemake -s hic.rules -c config.yaml --cores 4 --stats stats.txt --use-apptainer --apptainer-prefix ~/.sequana/apptainers --apptainer-args "-B /home:/home"
By default, the home is already set for you. Additional binding path can be set using environment variables e.g.:
export APPTAINER_BINDPATH=" -B /pasteur"
This pipelines requires the following executable(s):
- fastqc
- bwa
- chromap (implemented but still WIP so not really required)
- pairtools
- samtools
This pipeline runs hic in parallel on the input fastq files (paired or not). A brief sequana summary report is also produced.
Here is the latest documented configuration file to be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file.
| Version | Description |
|---|---|
| 0.0.1 | First release. |
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.