| 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 | Â |
 |  |  | 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 | Â | Â | Â | Â | Â |
methylation | √ | ProcessBismarAln, | Bismark, | Bscall | bicycle |
calling | Â | Bismark | MethylDackel | Â | analyzemethylation, GATK |
imputation of | - | METHimpute | - | - | - |
missing cytosines | Â | Â | Â | Â | Â |
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 | Â | Â | Â | bedGraph | Â |