The recently introduced Kallisto pseudoaligner has radically simplified the 
quantification of transcripts in RNA-sequencing experiments.  We offer 
cloud-scale RNAseq pipelines Arkas-Quantification, and Arkas-Analysis available 
within Illumina's BaseSpace cloud application platform which expedites Kallisto 
preparatory routines, reliably calculates differential expression, and performs 
gene-set enrichment of REACTOME pathways .  Due to inherit inefficiencies of 
scale, Illumina's BaseSpace computing platform offers a massively parallel 
distributive environment improving data management services and data importing. 
  Arkas-Quantification deploys Kallisto for parallel cloud computations and is 
conveniently integrated downstream from the BaseSpace Sequence Read Archive 
(SRA) import/conversion application titled SRA Import.  Arkas-Analysis annotates 
the Kallisto results by extracting structured information directly from source 
FASTA files with per-contig metadata, calculates the differential expression and 
gene-set enrichment analysis on both coding genes and transcripts. The Arkas 
cloud pipeline supports ENSEMBL transcriptomes and can be used downstream from 
the SRA Import facilitating raw sequencing importing, SRA FASTQ conversion, RNA 
quantification and analysis steps.