methurator 0.1.4

Python package designed to estimate sequencing saturation for reduced-representation bisulfite sequencing (RRBS) data.

🧬 methurator

Methurator is a Python package designed to estimate sequencing saturation for reduced-representation bisulfite sequencing (RRBS) data.

Although optimized for RRBS, methurator can also be used for whole-genome bisulfite sequencing (WGBS) or other genome-wide methylation data (e.g. EMseq). However, this data we advise you to use Preseq package.

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🧠 Dependencies and Notes

• methurator uses SAMtools and MethylDackel internally for BAM subsampling, thus they need to be installed.
• When --genome is provided, the corresponding FASTA file will be automatically fetched and cached.
• Temporary intermediate files are deleted by default unless --keep-temporary-files is specified.

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📦 Pip installation

pip install methurator

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🚀 Quick Start

Step 1 — Downsample BAM files

The downsample command performs BAM downsampling according to the specified percentages and coverage.

methurator downsample --genome hg19 --bam test_data/SRX1631721.markdup.sorted.csorted.bam

This command generates two summary files:

• CpG summary — number of unique CpGs detected in each downsampled BAM
• Reads summary — number of reads in each downsampled BAM

Example outputs can be found in tests/data.

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Step 2 — Plot the sequencing saturation curve

Use the plot command to visualize sequencing saturation:

methurator plot \
  --cpgs_file tests/data/cpgs_summary.csv \
  --reads_file tests/data/reads_summary.csv

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⚙️ Command Reference

🧩 downsample command

Argument	Description	Default
--bam	Path to a single .bam file.	—
--bamdir	Directory containing multiple BAM files.	—
--outdir	Output directory.	./output
--fasta	Path to the reference genome FASTA file. If not provided, it will be automatically downloaded based on --genome.	—
--genome	Genome used for alignment. Available: hg19, hg38, GRCh37, GRCh38, mm10, mm39.	—
--downsampling-percentages, -ds	Comma-separated list of downsampling percentages between 0 and 1 (exclusive).	0.1,0.25,0.5,0.75
--minimum-coverage	Minimum CpG coverage to consider for saturation. Can be a single integer or a list (e.g. 1,3,5).	3
--keep-temporary-files	If set, temporary files will be kept after analysis.	False

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📊 plot command

Argument	Description	Default
--cpgs_file	Path to the CpG coverage summary file.
--reads_file	Path to the reads coverage summary file.
--outdir	Output directory.	./output

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📘 Example Workflow

# Step 1: Downsample BAM file
methurator downsample --genome hg19 --bam my_sample.bam

# Step 2: Plot saturation curve
methurator plot \
  --cpgs_file output/cpgs_summary.csv \
  --reads_file output/reads_summary.csv