Incremental Mapping: the newMapping and Related Commands

2.15.3

This section describes the main commands of the GS Reference Mapper application, to be used when one or more Runs are to be mapped against a reference sequence or database, as part of a mapping project. These commands allow you to add Runs over time and incrementally align them to the reference; and to change the reference sequence and restart mapping without losing the data set of Runs. With these commands, the execution of the mapping and generation of the results can be controlled by command line options and configuration parameters (paralleling the equivalent controls in the GUI application). Such incremental mapping can be useful when, for example, you want to see intermediate mapping results on existing sequencing Runs to determine if you need to carry out further Runs to reach a desired depth of coverage, or just to monitor the project. Incremental mapping is also useful if you simply wish to create output using different output parameter settings.

Five commands are used in a mapping project: newMapping, setRef, addRun, removeRun and runProject. These are described in the subsections below.

2.15.3.1

The newMapping Command

The newMapping command is used to initiate a mapping project and set up a mapping project folder to contain the project data (see Section 2.15.1). Its command line structure is:

newMapping [option] [projdir]

…where:

•	[option] -cdna may be used; see Section 4.1

•	[projdir] is the optional name of the project directory

2.15.3.2

The setRef Command

The setRef command is used to assign the reference sequence(s) to which the reads from the sequencing Run(s) included in the project will be mapped. Its command line structure is:

setRef [projdir] refdesc…

…where each “refdesc” is one of the following:

•	reffasta: a FASTA file containing the reference sequence(s),

•	refdirname: a name or path for a directory containing the reference sequence (all FASTA files in the directory will be used in the reference),

•	refgenome: a GoldenPath genome name (see the third Note in the runMapping Section 2.15.2, above).

2.15.3.3

The addRun Command

The addRun command is used to add Read Data sets to existing mapping projects. Its command line structure is:

addRun [options] [MIDList@]filedesc…

…where:

•	“[options]” are zero or more of the command line options described in section 4.3

•	each “filedesc” is one of the following:

◦	sfffilename or

◦	[regionlist:]datadir or

◦	readfastafile

Input read size constraints: The reads input for the mapping computation must be shorter than 2000 bases per read (longer sequences are ignored) and longer than 50 bases (shorter sequences are ignored). When Paired End 454 Reads (SFF reads) are part of the project, reads between the value of the minlen parameter and 50 bp long will be mapped onto contigs formed by mapping longer reads to the reference during a later stage in the mapping process.

•

The addRun command can be executed multiple times for a mapping project (in any combination with the removeRun and runProject commands). When addRun is executed, it adds (not “resets”) the given Runs/regions or SFF files to the list of sequencing data used in the project. (It does not reset the list of sequence data). The reads used in the mapping (runProject, see section 2.15.3.5 below) are the union of the data from all executions of addRun for the project.

•	The commands addRun, removeRun, and runProject can be executed in any combination and in any order, in a mapping project.

2.15.3.4

The removeRun Command

The removeRun command is used to remove Read Data sets from existing mapping projects. Its command line structure is:

removeRun [projdir] (sffname or readfastafilepath)…

•

This command is more conveniently carried out from the GUI application. When called from the command line, it requires the SFF file name(s) given in the project sff sub-directory or the FASTA/FASTQ file name(s) given in the project configuration file 454MappingProject.xml. These names may not match the original names of the corresponding files or may not be known to the user, especially if the software had to rename any of them to ensure name uniqueness. The filenames of the SFF files in the sff sub-directory are assigned by the GS Reference Mapper application to ensure uniqueness for all the files, while trying to preserve the original names when possible.

•

The execution of this command does not physically remove the file(s) from the project sff sub-directory or from any existing mapping. The file(s) and the reads they contain are only marked for removal by the removeRun command, and are actually removed only the next time the project is computed (via the runProject command).

•	The commands addRun, removeRun, and runProject can be executed in any combination and in any order, in a mapping project.

2.15.3.5

The runProject Command

The runProject command performs the actual mapping computation for a project and generates the results of the mapping. Its command line structure is:

runProject [options] [projdir]