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Table 1 Table showing different features of MethylStar as compared to other BS-seq pipelines

From: MethylStar: A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing data

  Methylpy MethylStar methylseq gemBS Bicycle
Pipeline Features
Multi-threading  
language Python Python, shell, R Java C, Python Java
distribution github, PyPI GitHub Github GitHub Github
  (Apache license) (GNU GPL3) (MIT license) (GNU GPL3) (GNU GPL3)
Installation & pip install, install Docker, install Docker, Docker, Docker
configuration dependencies dependencies Singularity, Singularity  
    Conda   
User-interface - - - -
Single/paired-end
Input data Single-cell, WGBS, WGBS, Single-cell WGBS RRBS, WGBS, WGBS
  singlecell NOMe-seq, PBAT (PBAT)   PBAT  
Pipe steps
adapter trimming Cutadapt Trimmomatic TrimGalore - bicycle analyzemethylation
alignment bowtie/bowtie2 Bismark Bismark, gem3 bicycle align/
    bwa-meth   bowtie/bowtie2
remove PCR Picard Bismark Bismark, Picard Bscall bicycle analyzemethylation
duplicates      
methylation ProcessBismarAln, Bismark, Bscall bicycle
calling   Bismark MethylDackel   analyzemethylation, GATK
imputation of - METHimpute - - -
missing cytosines      
DMR calling - - - bicycle analyze
      differential
      methylation
SNP calling - - - Bscall -
Alignment QC - Bismark Qualimap
summary reports FastQC Bismark,
    MultiQC, Preseq   
Methylation BigWig BigWig, bedGraph - BigWig, BigWig
visualization     bedGraph  
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