https://github.com/open2c/inspectro-nf

https://github.com/open2c/inspectro-nf

Last synced: about 1 year ago
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• Host: GitHub
• URL: https://github.com/open2c/inspectro-nf
• Owner: open2c
• Created: 2023-05-05T20:12:59.000Z (about 3 years ago)
• Default Branch: main
• Last Pushed: 2023-11-23T00:46:31.000Z (over 2 years ago)
• Last Synced: 2025-04-24T01:13:50.523Z (about 1 year ago)
• Language: Python
• Size: 146 KB
• Stars: 7
• Watchers: 8
• Forks: 2
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • Citation: CITATION.cff

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README

          
# Inspectro 

[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg)](https://www.nextflow.io/)

[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)

[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)

[![DOI](https://zenodo.org/badge/636857069.svg)](https://zenodo.org/badge/latestdoi/636857069)

## Introduction

![Diagram of Inspectro pipeline](/assets/inspectro_subway_map.png)

Inspectro is a bioinformatics pipeline that characterizes long-range interaction profiles in Hi-C maps by spectral decomposition. The pipeline is built using Nextflow, a workflow tool that enables easy installation and reproducibility of the pipeline through Docker containers. 

This pipeline (v1.2) supports S3 files for bigwig/bigbed tracks.

Note: Local files are not currently supported.

Future update: Adding iGenomes, which will provide the option to use your own fasta file or one provided by iGenomes for the genome of your choice.

 

## Quick Start and Usage

1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`)

2. Install [`Docker`](https://docs.docker.com/engine/installation/) to implement environment for pipeline reproducibility.

Build the Docker image: `docker build -t open2c/inspectrov1.2:latest ./docker`

3. Place supplementary tab-delimited bigwig file with a header in `data/track_metadata.tsv` to include in graphical outputs. The following columns must be included:

* `Name`: a display name

* `ID`: a unique identifier to use in the database (can be the same as `Name`)

* `FileFormat`: must be the string `bigWig`

* `Path`: a local absolute path to the file

4. Add supplementary bigwig track names, sample name and genome assembly name to the params.yml file.

5. Finally, you can run the pipeline using:

  ```bash

  nextflow run main.nf \

      --config params.yml \

      --genome  \

      --meta track_metadata.tsv \

      --outdir  \

      --blacklist  \

      --mcool  \

      -profile docker

  ```

## Credits

Tarishi Pathak, Aleksandra Galitsyna, George Spracklin, Nezar Abdennur

## Citation

```bibtex

@article{spracklin2022diverse,

  title={Diverse silent chromatin states modulate genome compartmentalization and loop extrusion barriers},

  author={Spracklin, George and Abdennur, Nezar and Imakaev, Maxim and Chowdhury, Neil and Pradhan, Sriharsa and Mirny, Leonid A and Dekker, Job},

  journal={Nature Structural \& Molecular Biology},

  pages={1--14},

  year={2022},

  publisher={Nature Publishing Group}

}

```