NAME

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

DESCRIPTION

   USAGE:
              build_blast_atlas_all_vs_all -p DIR [Options]

   DESCRIPTION:
              This script generates several CCT projects automatically, and then it combines the results into  a
              single  montage  map.  The  montage consists of a separate map for each sequence of interest. This
              allows each sequence in a group of sequences to be visualized as the reference sequence.

              This command is used to first create a blast atlas all vs all project directory and then again  to
              generate  the  montage.  After  the  project has been created, place the genomes to compare in the
              comparison_genomes directory.

              [Optional] Make changes to the project_settings_multi.conf file 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:
       -p, --project DIR

              If  no  project exists yet, creates a new project directory. Otherwise, initiates map creation for
              the project.

   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 or
              if  creating  new  map sizes (see --map_size). Note that any changes in the .conf files related to
              blast will be ignored. This option will be ignored if  the  --start_at_map  or  --start_at_montage
              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. This option will be ignored if the --start_at_montage option is also
              provided.

       -g, --start_at_montage

              Start  at  montage  generation.  Skips  creating the individual maps.  Useful if changing how many
              columns the montage should have.

       -y, --columns INTEGER

              The number of columns to use in the montage image (Default: 4). If  the  maps  have  already  been
              drawn once, it is best to use this option with the --start_at_montage option.

       -h, --help

              Show this message.

   NOTES:
              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.