Blast2GO Command Line


A Functional Annotation Pipeline

The Blast2GO Command Line is a professional solution for flexible, high-performance and automatic functional annotation tasks. This Annotation Pipeline allows you to integrate and automate your functional annotation task in a flexible way. Generate high-quality results in a reproducible way directly integrated into your data analysis workflows.

High Performance

The command-line version of Blast2GO allows you to analyse large dataset on your performant computing servers will nearly no extra effort.


Easily integrate your functional annotation tasks within your custom analysis pipeline and run different analysis scenarios in parallel.

Automatic Data Generation

Generate all the statistics charts Blast2GO offers in an automatic fashion. This includes a summary report in PDF as well as images and text file formats.


Control the whole analysis with a simple configuration file. This allows you to set up different analysis strategies and reproduce the multiple scenarios for one or various datasets.


Run BLAST, InterProScan and the Blast2GO annotation offline on your own servers according to your security requirements. Take 100% control of data sources and versions you use throughout the analysis.


Main Features

Run Blast2GO on your own servers and control all analysis steps from the command line.

  • Automate your functional annotation
  • Reproduce your results in a consistent manner
  • Design advanced annotation strategies
  • Integrate Blast2GO into your existing analysis pipeline
  • Generate comprehensive PDF reports (see example report: Tomato)
  • Save all your results to specific project folders
  • Work consistent and effective once you found the right settings for your analysis. The Command Line offers a very detailed and explicatory property file
  • Run Blast locally or via Blast2GO CloudBlast
  • Run a remote InterProScan directly from within the Blast2GO command line
  • Extract Fasta sequences from a Reference Genome via a GFF or GTF file
  • Work offline. The Command Line supports easy Blast2GO database installation and updates
  • More detailed logging, additional export functions, etc ...


Licensing options

Several options are available to license the Blast2GO CommandLine depending on your setup setup scenario.

  • Single Server License: This static licence allows to install the CommandLine on one server/workstation. No paralell executions are allowed. To request a trial license please fill this form .
  • Floating Network License: This licence allows to run the CommandLine on a specified, flexible number of server within your organization via a Network License Server. Paralell executions are possible. MultiFor more information please write to: This email address is being protected from spambots. You need JavaScript enabled to view it.
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Scientific Impact of Blast2GO

Publications, Citations and Testimonials.