flemoine

Sratoolkit 2.5.7 + aspera-connect 3.6.2

subread 1.5.0-p2 for counting rna-seq reads (featurecounts, etc.)

samtools 1.3.1

STAR 2.5.1b for RNA-Seq read alignment

R-3.2.5 with packages for RNA-Seq: DESeq2, DEXSeq, HTSeq, limma

EMBOSS is "The European Molecular Biology Open Software Suite"

Bowtie 2 is an ultrafast tool for aligning sequencing reads to reference sequences.