From: ARPEGGIO: Automated Reproducible Polyploid EpiGenetic GuIdance workflOw
ARPEGGIO | QUMA | MOABS | QuasR | MethPipe | bicycle | RUbioSeq | WBSA | P3BSseq | Methy-Pipe | MethFlow | snakePipes | |
---|---|---|---|---|---|---|---|---|---|---|---|---|
Language | Python, R | HTML, Perl, Javascript | C++, Perl | R | C++ | Java | Perl | Perl, R | Python | Perl, R | Python, Perl, Java | Python, R |
Polyploid support | ✓ | X | X | X | X | X | X | X | X | X | X | X |
Diploid support | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
Quality check | ✓ | ✓ | ✓ | ✓ | ✓ | X | ✓ | ✓ | ✓ | X | X | ✓ |
Alignment | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
Statistical analyses | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | X | ✓ | ✓ | ✓ | ✓ | ✓ |
Methylation context | All | CpG only | All | All | All | All | All | All | All | All | ? | CpG only |
Downstream analyses | ✓ | X | X | ✓ | ✓ | X | X | ✓ | X | ✓ | ✓ | X |
Visualization | X | X | X | ✓ | ✓ | X | X | ✓ | X | ✓ | ✓ | X |
Reproducibility | ✓ | – | – | ✓ | – | ✓ | – | – | – | – | ✓ | ✓ |
Paper | – | [72] | [67] | [73] | [74] | [75] | [76] | [77] | [78] | [79] | [80] | [81] |