A Functional Annotation Pipeline: The Blast2GO Command Line is a professional solution to integrate flexible, high-performance and automatic functional annotation tasks. Generate high-quality results in a reproducible way directly integrated into your data analysis workflows. The Blast2GO Command Line (CLI) version allows combining BLAST and InterPro XML results, to perform the mapping against the GO (Gene Ontology) database and to assign the most suitable functional labels to the un-characterized sequence dataset. The command line allows running the GO analysis with a local database that can be easily set up from the command line. Additionally, the CLI allows performing GO-Slim and to generate over 25 different summary charts and a comprehensive PDF report of each analysis. The Command Line is based on the Blast2GO methodology, first published in 2005, [Conesa et al., 2005] for the functional annotation and analysis of gene or protein sequences. The method uses local sequence alignments (BLAST) to find similar sequences (potential homologues) for one up to hundreds of thousands of query sequences. The program extracts all GO terms associated with each of the obtained hits and returns an evaluated GO annotation for all query sequences. Enzyme codes are obtained by mapping to equivalent GOs and InterPro motifs can directly be added to the BLAST-based annotation. A basic annotation process with Blast2GO consists of 4 steps: blasting and InterProScan, GO mapping and functional annotation [Götz et al., 2008].