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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

Â