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gap4(1)


NAME

   gap4 - Genome Assembly Program (part of staden package)

SYNOPSIS

   gap4   [-ro]   [-maxseq   <number>]   [-maxdb  <number>]  [-skip_notes]
   [DATABASE_NAME.V]

DESCRIPTION

   Gap4 is a Genome Assembly Program. The program contains all  the  tools
   that  would  be  expected  from  an  assembly  program plus many unique
   features and a very easily used interface.  The  original  version  was
   described in Bonfield,J.K., Smith,K.F. and Staden,R. A new DNA sequence
   assembly program. Nucleic Acids Res. 24, 4992-4999 (1995)

   Gap4 is very big and powerful. Everybody employs a  subset  of  options
   and has their favourite way of accessing and using them. Although there
   is a lot of it, users are encouraged to go through  the  whole  of  the
   documentation once, just to discover what is possible, and the way that
   best suits their own work.  At  the  very  least,  the  whole  of  this
   introductory  chapter  should be read, as in the long run, it will save
   time.

OPTIONS

   -ro    Read-only

   -maxseq N
          Initial maximum total consensus length

   -maxdb N
          Initial maximum number of contigs + readings

   -(no_)check
          (Do not) run Check Database upon DB open

   -(no_)exec_notes
          (Do not) execute OPEN/CLOS notes upon database open

   -(no_)rawdata_note
          (Do not) use RAWD note instead of RAWDATA env. variable

   -(no_)csel
          (Do not) start up the contig selector upon db open

   -display
          X Display to use

   -bitsize N
          Specifies the aux file bitsize for new databases (32/64)

   -sync  Use synchronous mode for display server (debugging)

   --     End of argument list

SEE ALSO

   http://staden.sourceforge.net/manual/gap4_unix_2.html



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