NAME

       build_blast_atlas - visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences

DESCRIPTION

   USAGE:
              build_blast_atlas -i FILE [-p DIR] [Options] build_blast_atlas -p DIR [Options]

   DESCRIPTION:
              This  command  is  used to first create a blast atlas project directory and then again to generate
              maps.  Run this command with the '-i' option and a GenBank file to create a new project using  the
              GenBank file as the reference genome. Alternatively, a blank project can be created using the '-p'
              option, in which case a reference GenBank file will have to be  placed  in  the  reference_genomes
              directory.  After the project has been created, place the genomes to compare with the reference in
              the comparison_genomes directory.

              [Optional] Make changes to the *.conf  files  to  configure  how  the  maps  will  be  drawn.  Add
              additional GFF files to the features and analysis directories.

              Draw maps by running this command again with the '-p' option pointing to the project directory.

   REQUIRED ARGUMENTS:
       -i, --input FILE

              Sequence  file  in  GenBank format, with a .gbk extension. This option is only required when first
              creating a blast atlas project. The project directory will be named after  this  file  unless  the
              '-p' option is provided.

       -p, --project DIR

              Initiates map creation for the project. If no project exists yet, a blank project will be created.
              When used with the '-i' option, this will be where the project is created.  This  option  is  only
              required when creating the blast atlas maps.

   OPTIONAL ARGUMENTS:
       -m, --memory STRING

              Memory value for Java's -Xmx option (Default: 1500m).

       -c, --custom STRING

              Custom settings for map creation.

       -b, --max_blast_comparisons INTEGER

              Maximum number of comparison genomes to display (Default: 100).

       -z, --map_size STRING

              Size  of  custom  maps to create. For quickly regenerating new map sizes, use this option with the
              --start_at_xml  option.  Possible  sizes  include  small/medium/large/x-large  or  a   combination
              separated  by  commas  (e.g.   small,large). The size(s) provided will override the size(s) in the
              configuration files.

       -x, --start_at_xml

              Jump to XML generation. Skips performing blast, which  can  speed  map  generation  if  blast  has
              already  been  done. This option is for creating new maps after making changes to the .conf files.
              Note that any changes in the .conf files related to blast will be ignored.  This  option  will  be
              ignored if the --start_at_map option is also provided.

       -r, --start_at_map

              Start  at  map  generation. Skips performing blast and generating XML. Useful if manual changes to
              the XML files have been made or if creating new map sizes (see --map_size).

       -h, --help

              Show this message.

   NOTE:
              This script will likely not work if there are spaces in the path to the project directory  because
              the NCBI tool 'formatdb' cannot handle such paths.

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.