Table 1.

Table of the times and the RAM memory peaks reached during the RNA-Seq analysis for the eight pipelines

	Alignment	Quantification	DEA	Time (h)	RAM (Gb)
1° pipeline	TopHat2	Cufflinks	cummeRbund	35	3.3
2° pipeline	Hisat2	StringTie	Ballgown	4	4.3
3° pipeline	Hisat2	featureCounts	DESeq2	4	4.3
4° pipeline	Hisat2	featureCounts	edgeR	4	4.3
5° pipeline	STAR	Cufflinks	cummeRbund	5	30
6° pipeline	STAR	featureCounts	DESeq2	4	30
7° pipeline	STAR	featureCounts	edgeR	4	30
8° pipeline	Kallisto	Kallisto	Sleuth	2	2.2

The longest pipeline was found to be TopHat2-Cufflinks-cummeRbund, while the shorter kallisto-sleuth. The RAM memory peaks are maintained in all cases except for STAR pipelines below 5 Gb