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gap5 - Online in the Cloud

Run gap5 in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command gap5 that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


gap5 - Genome Assembly Program (part of staden package)

SYNOPSIS


gap5 [-ro] [-maxseq <number>] [-maxdb <number>] [-skip_notes] [DATABASE_NAME.V]

DESCRIPTION


Gap5 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)

Gap5 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

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