Grape RNA-Seq analysis pipeline environment

CRGResearchers at the Centre for Genomic Regulation (CRG) and UPF, Spain have developed a pipeline for processing and analyzing RNA-Seq data, that they have named Grape (Grape RNA-Seq Analysis Pipeline Environment). Grape supports raw sequencing reads produced by a variety of technologies, either in Fasta or FastQ format, or as prealigned reads in SAM/BAM format. A minimal Grape configuration consists of the file location of the raw sequencing reads, the genome of the species, and the corresponding gene and transcript annotation.Grape first runs a set of quality control (QC) steps, and then aligns the reads to the genome, a step that is omitted for prealigned read formats. Grape next estimates gene and transcript expression levels, calculates exon inclusion levels, and identifies novel transcripts. Grape can be run on a single computer or in parallel on a computer cluster. It is distributed with specific mapping and quantification tools, but given its modular design, any tool supporting popular data inter-change formats, can be integrated.

AVAILABILITY – Grape can be obtained from the Bioinformatics and Genomics website at:

  • Knowles D, Röder M, Merkel A, Guigó R. (2013) Grape RNA-Seq analysis pipeline environment. Bioinformatics [Epub ahead of print]. [abstract]