Overview
TwistNext is a comprehensive Nextflow pipeline designed for the analysis of Twist NGS Methylation data, including quality control, alignment, methylation calling, differential methylation analysis, and post-processing. It integrates cutting-edge tools and custom scripts to deliver accurate and insightful results.
Highlights
The pipeline includes:
- READ_PROCESSING: Quality control and trimming with FastQC and Trim Galore.
- BISMARK_ANALYSIS: Alignment, deduplication, methylation calling, and reporting using Bismark.
- QC_REPORTING: MultiQC for aggregated reporting.
- DIFFERENTIAL_METHYLATION: EdgeR and MethylKit for statistical analysis.
- POST_PROCESSING: Visualization and summary generation.
| Step | Workflow |
|---|---|
| Generate Reference Genome Index | Bismark |
| Raw Data QC | FastQC |
| Align Reads | Bismark (bowtie2) |
| Extract Methylation Calls | Bismark |
| Differential Methylation Analysis | EdgeR/MethylKit |
| Post-Processing | ggplot2 |
Pipeline Schema
Usage
nextflow run main.nf \
-profile singularity \
--sample_sheet Sample_sheet_twist.csv \
--genome_fasta /path/to/genome.fa \
--diff_meth_method edger \
--outdir /path/to/output
Example of Sample_sheet.csv:
| Sample ID | Group | Read 1 | Read 2 |
|---|---|---|---|
| SN09 | Healthy | FASTQ/SN09/SL1_S9_R1_001.fastq.gz | FASTQ/SN09/SL1_S9_R2_001.fastq.gz |
| SN10 | Disease | FASTQ/SN10/SL2_S10_R1_001.fastq.gz | FASTQ/SN10/SL2_S10_R2_001.fastq.gz |
Credits
Author: Jyotirmoy Das
DOI: 10.5281/zenodo.14204260
Citation
Das, J. (2024). TwistNext (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.14204260