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auto-rename: TwistMethNext → TwistMethylFlow (docs, README, remote updated)
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‎README.md‎

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![](artworks/twistmethnext.png)
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[![DOI](https://zenodo.org/badge/490592846.svg)](https://doi.org/10.5281/zenodo.14204261)
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[![GitBook Docs](https://img.shields.io/badge/docs-GitBook-blue?logo=gitbook)](https://jyotirmoys-organization.gitbook.io/TwistMethNext)
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[![build-docs](https://github.com/JD2112/TwistMethNext/actions/workflows/build-docs.yml/badge.svg?branch=main)](https://github.com/JD2112/TwistMethNext/actions/workflows/build-docs.yml)
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[![GitHub Invite Collaborators](https://img.shields.io/badge/Invite-Collaborators-blue?style=for-the-badge&logo=github)](https://github.com/JD2112/TwistMethNext/settings/access)
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[![GitBook Docs](https://img.shields.io/badge/docs-GitBook-blue?logo=gitbook)](https://jyotirmoys-organization.gitbook.io/TwistMethylFlow)
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[![build-docs](https://github.com/JD2112/TwistMethylFlow/actions/workflows/build-docs.yml/badge.svg?branch=main)](https://github.com/JD2112/TwistMethylFlow/actions/workflows/build-docs.yml)
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[![GitHub Invite Collaborators](https://img.shields.io/badge/Invite-Collaborators-blue?style=for-the-badge&logo=github)](https://github.com/JD2112/TwistMethylFlow/settings/access)
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[![wakatime](https://wakatime.com/badge/user/fe95275f-909a-4147-a45d-624981173898/project/a44415f0-a274-4c3b-a59a-f8e1067c0fc1.svg)](https://wakatime.com/badge/user/fe95275f-909a-4147-a45d-624981173898/project/a44415f0-a274-4c3b-a59a-f8e1067c0fc1)
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- Java (>=8)
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## Usage
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1. User can start from the FASTQ files or Bismark aligned BAM files. Find the details on the [manual](https://jyotirmoys-organization.gitbook.io/TwistMethNext)
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1. User can start from the FASTQ files or Bismark aligned BAM files. Find the details on the [manual](https://jyotirmoys-organization.gitbook.io/TwistMethylFlow)
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2. User can choose to run the differential methylation analysis - either EdgeR or MethylKit or both. Find the details on the [manual](https://jyotirmoys-organization.gitbook.io/TwistMethNext)
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2. User can choose to run the differential methylation analysis - either EdgeR or MethylKit or both. Find the details on the [manual](https://jyotirmoys-organization.gitbook.io/TwistMethylFlow)
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3. User can also use `--skip_diff_meth` to avoid the differential methylation analysis.
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```
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# when using the reference genome indexing, --genome_fasta
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nextflow run JD2112/TwistMethNext \
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nextflow run JD2112/TwistMethylFlow \
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-profile singularity \
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--sample_sheet Sample_sheet_twist.csv \
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--genome_fasta /data/reference_genome/hg38/hg38.fa \
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--run_both_methods \
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--gtf_file /data/Homo_sapiens.GRCh38.104.gtf \
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--refseq_file /data/hg38_RefSeq.bed.gz \
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--outdir Results/TwistMethNext_both
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--outdir Results/TwistMethylFlow_both
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# if you already have the bisulfite genome index, --bismark_index
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nextflow run JD2112/TwistMethNext \
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nextflow run JD2112/TwistMethylFlow \
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-profile singularity \
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--sample_sheet Sample_sheet_twist.csv \
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--bismark_index /data/reference_genome/hg38/ \
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--run_both_methods \
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--gtf_file /data/Homo_sapiens.GRCh38.104.gtf \
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--refseq_file /data/hg38_RefSeq.bed.gz \
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--outdir /mnt/Results/TwistMethNext_both
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--outdir /mnt/Results/TwistMethylFlow_both
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```
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```
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# when using the reference genome indexing, --genome_fasta
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nextflow run JD2112/TwistMethNext \
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nextflow run JD2112/TwistMethylFlow \
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-profile singularity \
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--sample_sheet Sample_sheet_twist.csv \
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--genome_fasta /data/reference_genome/hg38/hg38.fa \
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--diff_meth_method edger \
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--refseq_file /data/hg38_RefSeq.bed.gz \
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--outdir Results/TwistMethNext_edgeR
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--outdir Results/TwistMethylFlow_edgeR
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# if you already have the bisulfite genome index, --bismark_index
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nextflow run JD2112/TwistMethNext \
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nextflow run JD2112/TwistMethylFlow \
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-profile singularity \
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--sample_sheet Sample_sheet_twist.csv \
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--bismark_index /data/reference_genome/hg38/ \
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--diff_meth_method edger \
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--refseq_file /data/hg38_RefSeq.bed.gz \
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--outdir /mnt/Results/TwistMethNext_edgeR
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--outdir /mnt/Results/TwistMethylFlow_edgeR
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```
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### `--diff_meth_method`: MethylKit
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```
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# when using the reference genome indexing, --genome_fasta
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nextflow run JD2112/TwistMethNext \
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nextflow run JD2112/TwistMethylFlow \
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-profile singularity \
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--sample_sheet Sample_sheet_twist.csv \
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--genome_fasta /data/reference_genome/hg38/hg38.fa \
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--diff_meth_method methylkit \
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--gtf_file /data/Homo_sapiens.GRCh38.104.gtf \
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--outdir Results/TwistMethNext_methylKit
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--outdir Results/TwistMethylFlow_methylKit
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# if you already have the bisulfite genome index, --bismark_index
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nextflow run JD2112/TwistMethNext \
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nextflow run JD2112/TwistMethylFlow \
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-profile singularity \
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--sample_sheet Sample_sheet_twist.csv \
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--bismark_index /data/reference_genome/hg38/ \
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--diff_meth_method methylkit \
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--gtf_file /data/Homo_sapiens.GRCh38.104.gtf \
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--outdir Results/TwistMethNext_methylKit
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--outdir Results/TwistMethylFlow_methylKit
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```
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## Options:
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## HELP
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```
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nextflow run JD2112/TwistMethNext --help --outdir .
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nextflow run JD2112/TwistMethylFlow --help --outdir .
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```
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Find the details on the [manual](https://jd2112.github.io/TwistMethNext/)
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Find the details on the [manual](https://jd2112.github.io/TwistMethylFlow/)
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## Credits
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- Main Author:
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## Citation
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Das, J. (2024). TwistMethNext (v1.0.0). Zenodo. [https://doi.org/10.5281/zenodo.14204261](https://doi.org/10.5281/zenodo.14204261)
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Das, J. (2024). TwistMethylFlow (v1.0.0). Zenodo. [https://doi.org/10.5281/zenodo.14204261](https://doi.org/10.5281/zenodo.14204261)
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## HELP/FAQ/Troubleshooting
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Please check the [manual](https://jd2112.github.io/TwistMethNext/) for details.
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Please check the [manual](https://jd2112.github.io/TwistMethylFlow/) for details.
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Please create [issues](https://github.com/JD2112/TwistMethNext/issues) on github.
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Please create [issues](https://github.com/JD2112/TwistMethylFlow/issues) on github.
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## License(s)
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[GNU-3 public license](https://github.com/JD2112/TwistMethNext/blob/v1.0.3/LICENSE).
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[GNU-3 public license](https://github.com/JD2112/TwistMethylFlow/blob/v1.0.3/LICENSE).
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## Acknowledgement
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‎docs/credits.md‎

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| Role | Name & Link | Description |
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|--------------|------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------|
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| **Main Author** | [Jyotirmoy Das](https://github.com/JD2112) | Lead designer, developer, and overall coordinator for the **TwistMethNext** pipeline. |
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| **Main Author** | [Jyotirmoy Das](https://github.com/JD2112) | Lead designer, developer, and overall coordinator for the **TwistMethylFlow** pipeline. |
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| **Maintainer** | [Jyotirmoy Das](https://github.com/JD2112) | Actively maintaining the pipeline, fixing bugs, and implementing new features. |
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| **Contributors**| [All Contributors](https://github.com/JD2112/TwistMethNext/pulls) | Thanks to everyone who helped in development, testing, and enhancement. Contributions welcome! |
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| **Contributors**| [All Contributors](https://github.com/JD2112/TwistMethylFlow/pulls) | Thanks to everyone who helped in development, testing, and enhancement. Contributions welcome! |
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## 📄 Citation
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If you use **TwistMethNext** in your work, please cite:
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If you use **TwistMethylFlow** in your work, please cite:
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> Das, J. (2024). *TwistMethNext (v1.0.0)*. Zenodo. [https://doi.org/10.5281/zenodo.14204261](https://doi.org/10.5281/zenodo.14204261)
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> Das, J. (2024). *TwistMethylFlow (v1.0.0)*. Zenodo. [https://doi.org/10.5281/zenodo.14204261](https://doi.org/10.5281/zenodo.14204261)
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## ❓ Help, FAQ, Troubleshooting
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- Refer to the [User Manual](index.md) for detailed usage instructions and guidance.
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- For bug reports, questions, or feature requests, please open an [issue on GitHub](https://github.com/JD2112/TwistMethNext/issues).
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- For bug reports, questions, or feature requests, please open an [issue on GitHub](https://github.com/JD2112/TwistMethylFlow/issues).
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- **National Academic Infrastructure for Supercomputing in Sweden (NAISS)**
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> The computations/data storage were enabled by resources provided by the National Academic Infrastructure for Supercomputing in Sweden (NAISS), partially funded by the Swedish Research Council through grant agreement no. 2022-06725.
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These institutions provided invaluable resources and support for the development and testing of the TwistMethNext pipeline.
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These institutions provided invaluable resources and support for the development and testing of the TwistMethylFlow pipeline.
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### Additional Thanks
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‎docs/index.md‎

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# TwistMethNext Documentation
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# TwistMethylFlow Documentation
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Welcome to the TwistMethNext documentation. This Nextflow pipeline is designed for the analysis of Twist NGS Methylation data, encompassing quality control, alignment, methylation calling, differential methylation analysis, and post-processing.
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Welcome to the TwistMethylFlow documentation. This Nextflow pipeline is designed for the analysis of Twist NGS Methylation data, encompassing quality control, alignment, methylation calling, differential methylation analysis, and post-processing.
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![Pipeline Schematic](./images/Figure%201.png)
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‎docs/overview.md‎

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TwistMethNext integrates various tools and custom scripts to provide a comprehensive analysis workflow for Twist NGS Methylation data.
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TwistMethylFlow integrates various tools and custom scripts to provide a comprehensive analysis workflow for Twist NGS Methylation data.
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| Step | Tool/Software | Description |
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|---------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------|

‎docs/references.md‎

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# Citations
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### TwistMethNext
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>**Das, J.** (2024). *TwistMethNext (v1.0.0)*. Zenodo. [https://doi.org/10.5281/zenodo.14204261](https://doi.org/10.5281/zenodo.14204261)
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### TwistMethylFlow
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>**Das, J.** (2024). *TwistMethylFlow (v1.0.0)*. Zenodo. [https://doi.org/10.5281/zenodo.14204261](https://doi.org/10.5281/zenodo.14204261)
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## Pipeline tools
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‎docs/usage.md‎

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## Run NextFlow
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--outdir Results/TwistMethylFlow_both
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‎mkdocs.yml‎

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site_name: TwistMethNext
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site_name: TwistMethylFlow
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site_description: A Nextflow-based DNA Methylation Data Analysis Pipeline for Twist NGS data
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site_author: Jyotirmoy Das
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repo_url: https://github.com/JD2112/TwistMethNext
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repo_url: https://github.com/JD2112/TwistMethylFlow
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