Table 1.

Comparing PipeOne with two other pipelines, RNACocktail and VIPER.

	PipeOne	RNACocktail	VIPER
Raw data processing
Quality control	√	x	√
Alignment	√	√	√
Transcriptome reconstruction	√	√	x
Gene quantification	√	√	√
Novel lncRNA prediction	√	x	x
CircRNA prediction	√	x	x
Gene quantification	√	√	√
Fusion prediction	√	√	√
Variant calling	√	√	√
RNA editing prediction	√	√	x
Retrotranscriptome	√	x	x
Alternative splicing	√	x	x
viral DNA detection	x	x	√
Long-read	x	√	x
Downstream analysis
Result visualization	x	x	√
Differential expression analysis	x	√	√
Pathway analysis	x	x	√
Batch correction	x	x	√
immunological analysis	x	x	√
Virus analysis	x	x	√
Feature prioritization	√	x	x
subtyping/clustering	√	x	√
Multi-modal integration	√	x	x
Runtime
Management systems	Nextflow	Python	Snakemake
Resume	√	x	√
Parrallel	√	x	√
Docker	√	√	x
Conda	√	√	√
Singularity	√	x	√