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

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

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]
  1. 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