EuGene-PP: a next-generation automated annotation pipeline for prokaryotic genomes

Abstract

It is now easy and increasingly usual to produce oriented RNA-Seq data as a prokaryotic genome is being sequenced. However, this information is usually just used for expression quantification. EuGene-PP is a fully automated pipeline for structural annotation of prokaryotic genomes integrating protein similarities, statistical information and any oriented expression information (RNA-Seq or tiling arrays) through a variety of file formats to produce a qualitatively enriched annotation including coding regions but also (possibly antisense) non-coding genes and transcription start sites.

Availability and implementation: EuGene-PP is an open-source software based on EuGene-P integrating a Galaxy configuration. EuGene-PP can be downloaded at eugene.toulouse.inra.fr.