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.