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