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.