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wgbstools - suite for DNA methylation sequencing data representation, visualization, and analysis

wgbstools is an extensive computational suite tailored for bisulfite sequencing data. It allows fast access and ultra-compact representation of high-throughput data, as well as machine learning and statistical analysis, and informative visualizations, from fragment-level to locus-specific representations.

It converts data from standard formats (e.g., bam, bed) into tailored compact yet useful and intuitive formats (pat, beta). These can be visualized in terminal, or analyzed in different ways - subsample, merge, slice, mix, segment and more.

alt text This project is developed by Netanel Loyfer and Jonathan Rosenski in Prof. Tommy Kaplan's lab at the Hebrew University, Jerusalem, Israel.

Quick start

Installation

# Clone
git clone https://github.com/nloyfer/wgbs_tools.git
cd wgbs_tools

# compile
python setup.py

Genome configuration

At least one reference genome must be configured (takes a few minutes).

wgbstools init_genome GENOME_NAME
# E.g, 
wgbstools init_genome hg19
wgbstools init_genome mm9

wgbstools downloads the requested reference FASTA file from the UCSC website. If you prefer using your own reference FASTA, specify the path to the FASTA as follows.

wgbstools init_genome GENOME_NAME --fasta_path /path/to/genome.fa

Dependencies

  • python 3+, with libraries:
    • pandas version 1.0+
    • numpy
    • scipy
  • samtools
  • tabix / bgzip

Dependencies for some features:

  • bedtools

Usage examples

Now you can generate pat.gz and beta files out of bam files:

wgbstools bam2pat Sigmoid_Colon_STL003.bam
# output:
# Sigmoid_Colon_STL003.pat.gz
# Sigmoid_Colon_STL003.beta

Once you have pat and beta files, you can use wgbstools to visualize them. For example:

wgbstools vis Sigmoid_Colon_STL003.pat.gz -r chr3:119528843-119529245

wgbstools vis *.beta -r chr3:119528843-119529245 --heatmap

Deconvolution

To deconvolve tissues or blood samples, see our UXM software

References

If you are using wgbstools, please cite:
Loyfer et al. (2024) ‘wgbstools: A computational suite for DNA methylation sequencing data representation, visualization, and analysis’, bioRxiv ,2024.
[GEO GSE186458 | Genome browser sessions: hg19 | hg38]