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