Table 1 Comparison of Transcriptome Analysis Pipelines
Tool/platform | Graphical user interface (GUI) | Workflow | DEG detection | Scalable (cluster) | Hosting | Installation | Reproducible runs | Automatic comprehensive report with statistics | Structured output folders | Bulk MARS-Seq | NGS tools other than for DE | Ref |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
Chipster | Yes | user defined | Yes | Yes | Local, Remote server and cloud | Medium (requires virtualization sw) | Yes | No | No | No | Yes | 19 |
RNACocktail | No | predefined | Yes | No | Local | Easy (Docker) | Yes | No | No | No | Yes | 20 |
hppRNA-a | No | predefined | Yes | Yes | Local | Medium (Installation script) | Yes | No | Yes | No | Yes | 21 |
aRNApipe | No | predefined | No | Yes | Local | Medium | Yes | Partial (no DEG) | Yes | No | Yes | 22 |
Galaxy | Yes | user defined | Yes | Yes | Local, Remote server and cloud | Complex | Yes | No | No | No | Yes | 23 |
Illumina BaseSpace | Yes | predefined | Yes | Yes | Remote (requires a fee) | NA | Yes | Partial | Yes | No | Yes | 24 |
docker4seq | Yes | predefined | Yes | Yes | Local | Easy (Docker) | Yes | No | Yes | No | Yes | 25 |
UTAP | Yes | predefined | Yes | Yes | Local | Easy (Docker) | Yes | Yes | Yes | Yes | No | NA |