This section gives a quick guide on the parameters used in Blast2GO CLI. Some command examples will be given in the end of the detailed description.

Load or import data commands:

• loadfasta <path> Path to fasta file. Activate -protein option when working with amino acids.
• loadblast <path> Load Blast .xml results (pre 2.2.31) -outfmt 5
• loadblast31 <path> Load Blast .xml/.json/.zip results (2.2.31+) -outfmt 13/14/15/16
• loadips48 <path> Load InterProScan 4.8 data file or folder
• loadips50 <path> Load InterProScan 5.0+ data file or folder
• loadannot <path> Load a .annot file
• loadb2g <path> Load a Blast2GO .b2g file
• loadbox <path> Load an OmicsBox .box file

Analysis commands:

• mapping Run the Gene Ontology mapping.
• annotation Run the Blast2GO Annotation algorithm.
• ecmapping Map Annotated GOs to their Enzyme Codes (Included when -annotation is set)
• goslim <path> Run goslim using an *.obo file. Possible subset obo files can either be downloaded from http://geneontology.org/page/go-slim-and-subset-guide, or customized by hand with OBO-Edit2.
• cloudblast <cloudkey> Run CloudBlast via webservice. This requires a working internet connection and a valid CloudBlast key with a positive balance.
• cloudunitbalance <cloudkey> Print the BioBam Bioninformatics Cloud computation unit balance. This requires a working internet connection.
• extractfasta <path> Extract features from a fasta reference to a fasta file (path). Needs configuration in the properties file.
• ips <email> Run InterPro via webservice. This requires a working internet connection, a valid email address and that your data-set contains sequence data.
• cloudips <cloudkey> Run InterPro for your nucleotide or amino acid sequences via the BioBam Bioinformatics Cloud Platform. This requires a working internet connection and a valid Cloud key with a positive balance.
• localblast <path> Run Blast ver. 2.4.0+ against a local database. Necessary Blast binaries will be downloaded to the indicated folder, if not provided. It is necessary is a correctly configured local blast database (properties file).

Save or export commands:

• saveannot <path> Save the functional annotations (Gene Ontology terms and Enzymes) as .annot
• savebox <path> Save the project as .box
• savelog <path> Save the log to a specified file.
• savelorf <path> Convert nucleotide sequences (FASTA format) into amino acid sequences (longest Open Reading Frame, FASTA format). This function may be used to prepare a FASTA file for a local InterProScan run.
• savereport <path> Create .pdf report
• saveseqtable <path> Save your data as it would be shown in OmicsBox (tab-separated)
• statistics <charts> Provide a comma-separated list of desired statistical charts (-statistics without options to get a list of all available charts). ’-statistics all’ will try to export all statistics that are available. The option -nameprefix will be ignored.
• exportgeneric <path> Export sequence data in tabular format for post processing

Other Options:

• createproperties <path> The default properties file will be created here.
• createkeyfile Create a file which contains a unique ID for your computer. This file is nessesary to issue license keys.
• enzymedat <path> Provide a specific version of enzyme.dat (ftp://ftp.expasy.org/databases/enzyme/enzyme.dat).
• enzclass <path> Provide a specific version of enzclass.txt (ftp://ftp.expasy.org/databases/enzyme/enzclass.txt).
• help Display this message
• nameprefix <name> Prefix for any output filenames in case you do not specifiy a path (default: b2g_project)
• properties <path> Properties file (mandatory)
• showlicenseinfo Show details about the currently available license.
• tempfolder <path> Temporary folder (default: System temp folder)
• useobo <path> The obo file to use for annotation, some statistics and various file im- and exports. Download the latest version from http://data.biobam.com/b2g_res/obo_files/go_latest.obo.gz
• workspace <path> Workspace folder, e.g. where the results will be saved if not specified (default: current folder)