https://github.com/dohlee/snakemake-hic-processing

Hi-C processing pipeline in snakemake.
https://github.com/dohlee/snakemake-hic-processing

bioinformatics hi-c pipeline reproducible-research snakemake snakemake-pipeline workflow

Last synced: 7 days ago
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Hi-C processing pipeline in snakemake.

• Host: GitHub
• URL: https://github.com/dohlee/snakemake-hic-processing
• Owner: dohlee
• Created: 2022-06-10T05:07:34.000Z (over 2 years ago)
• Default Branch: master
• Last Pushed: 2022-06-10T05:09:40.000Z (over 2 years ago)
• Last Synced: 2024-01-27T22:35:52.089Z (10 months ago)
• Topics: bioinformatics, hi-c, pipeline, reproducible-research, snakemake, snakemake-pipeline, workflow
• Language: Python
• Homepage:
• Size: 6.84 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# snakemake-hic-processing

Hi-C processing pipeline in snakemake.

This pipeline takes cares of (optional) download of raw sequencing reads from sequencing read archives, alignment using `bwa`, `.pairs` or `.pairsam` file generation and pair filtering using `pairtools`, and finally contact matrix generation using `cooler`.

## Quickstart

1. Clone the repo.

```

$ git clone https://github.com/dohlee/snakemake-hic-processing.git

$ cd snakemake-hic-processing

```

2. Modify the configuration `config.yaml` and `manifest.csv` as you want.

3. Create conda environment for this pipeline and run it. Consider using `mamba` if downloading packages takes long time. 

```

$ conda env create -f environment.yaml

```

## See also

This pipeline is mostly similar to the official Hi-C Processing Pipeline in 4D nucleome project: https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline. See also the official github repository https://github.com/4dn-dcic/docker-4dn-hic/tree/v43.