The GS De Novo Assembler Command Line Interface

1. GS De Novo Assembler : 1.13 The GS De Novo Assembler Command Line Interface

1.13	The GS De Novo Assembler Command Line Interface

1.13.1 Working with Project Folders and Data Files

1.13.2 One-Step Assembly: the runAssembly Command

1.13.3 Incremental Assembly: the newAssembly and Related Commands

The GS De Novo Assembler CLI commands for single shot assembly of reads can be launched using the following commands:

runAssembly [options] [filedesc]

For incremental assembly via the CLI, a project directory structure is created to organize the files of the incremental build of the project data. The following commands are used for incremental assembly projects;

newAssembly [-cdna] projdir

addRun [options: -p, -lib, -mcf] [projdir] filedesc

removeRun [projdir] filedesc

runProject [options] [projdir]

For all of these commands;

•	The arguments in brackets [ ] are optional.

•	‘options’ refers to the specific command options available.

•	‘filedesc’ is one of the following:

•	an sff filename

•	a [regionlist:]datadir

•	a read FASTA file

•

any of the above prepended by an [MIDList@] specification where each “MIDList” is a multiplexing information string used to filter the set of file reads to be used in the assembly (If MIDs were used in the generation of the read data file, then an MIDList string must be specified in order for the assembler to properly handle the file’s reads.) For details about using MIDs, see section 4.7.

•	‘projdir’ is the path of the data analysis project directory.

Some of the command line options for Assembly are mutually exclusive, for obvious functional reasons. See section 4.5 for a list of these options.