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Table 1 Comparison of Transcriptome Analysis Pipelines

From: UTAP: User-friendly Transcriptome Analysis Pipeline

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