Blast2GO Command Line Tools

Blast2GO Command Line Tools, developed by BioBam, is a professional functional annotation pipeline designed for bioinformaticians and researchers who need to execute and automate the Blast2GO Functional Annotation Methodology via the command line. It is built for high-performance environments, enabling large-scale genomic dataset analysis on dedicated computing servers with minimal additional effort. The solution is suitable for academic, government, non-profit, and commercial organisations seeking reproducible, automated, and secure annotation workflows.

The tool allows users to integrate functional annotation tasks directly into existing data analysis pipelines, run multiple analysis scenarios in parallel, and generate high-quality, reproducible results. All analysis steps are controlled through a simple configuration file, making it straightforward to define, replicate, and compare different annotation strategies across one or multiple datasets.

Key Capabilities

• Automate functional annotation tasks end-to-end from the command line
• Reproduce results consistently using a detailed and explicatory property/configuration file
• Design and execute advanced annotation strategies across multiple scenarios
• Integrate seamlessly into existing custom analysis pipelines
• Generate comprehensive PDF summary reports, statistics charts, and results in image and text file formats automatically
• Save all results to specific project folders for organised data management
• Run BLAST locally or via Blast2GO CloudBlast
• Run remote InterProScan directly from within the Blast2GO command line, including Cloud InterProScan support
• Extract FASTA sequences from a reference genome using GFF or GTF files
• Work fully offline with easy local Blast2GO database installation and updates
• Retrieve Enzyme Codes from annotated Gene Ontology terms via EC mapping
• Export data in customised CSV formats using the Generic Export Function, including Enzyme Codes in annotation exports
• More detailed logging and additional export functions compared to the desktop version

Security and Data Control

• Run BLAST, InterProScan, and the Blast2GO annotation pipeline entirely offline on your own servers
• Maintain 100% control over data sources and software versions used throughout the analysis
• Operate in compliance with your organisation's security requirements

Licensing Options

• Single Server Licence: A static licence permitting installation on one server or workstation; parallel executions are not permitted under this licence
• Floating Network Licence: Allows the command line tool to run on a specified, flexible number of servers within an organisation via a Network Licence Server; parallel executions are supported
• Licences are available for Academic/Government/Non-Profit organisations (60% discount) and Commercial entities
• Updates and support packages are available for one, two, or three years
• A fully functional trial version is available for download via email request

System Requirements

• Compatible with all three major platforms: Linux, Mac OS, and Windows
• Requires Java 11 or higher
• Minimum 1 GB of RAM recommended
• A MongoDB server (version 3.4.6 or higher) is required for a local Blast2GO database

Blast2GO Command Line Tools are actively maintained by BioBam, with a version history reflecting ongoing improvements including Cloud InterProScan integration, MongoDB-based GO mapping, floating licence support, enhanced PDF reporting, improved file handling, and compatibility fixes across Linux, Mac, and Windows environments.