SePIA: RNA and small RNA sequence processing, integration, and analysis

Table 1 Command-line executable software readily implemented in the SePIA workflow and used with the case studies

Module	Component	Software	Reference
Preprocessing	Adaptor and quality trimming	FastX-Toolkit	hannonlab.cshl.edu/ fastx_toolkit/
		Trimmomatic	[62]
		Trim Galore	www.bioinformatics. babraham.ac.uk/ projects/trim_galore/
	Quality statistics	FastQC ^a	www.bioinformatics. babraham.ac.uk/ projects/fastqc
Read mapping	Align sequences to a reference	BWA	[63]
		Tophat	[64]
		Bowtie	[13]
		Bowtie2	[65]
		STAR	[7]
	Alignment sorting and conversion	SAMtools ^a	[66]
		Picard tools ^a	broadinstitute.github. io/picard
	Alignment statistics	RNA-SeQC	[67]
		RSeQC	[68]
Expression	Mapped reads quantification	HTSeq	[69]
		Cufflinks	[70]
Analysis	Variant calling	Bambino	[35]
	and annotation	ANNOVAR	[71]
	Differential expression	Cuffdiff	[18]
	R bioconductor packages for differential expression	DESeq	[15]
		DESeq2	[72]
		DEXseq	[73]
		EdgeR	[14]
	novel miRNA discovery	miRanalyzer	[74]
		miRDeep2	[75]
miRNA-mRNA integration	R package for SQLite query	sqldf ^a	[76]
	Pathway impact analysis	SPIA	[77]

Software marked with ^a are mandatory requirements for the minimum execution of a module. A list of software pre-installed within SePIA’s Docker image and the full range of currently available components can be accessed through the website