Options Specific to Assembly

4.2	Options Specific to Assembly

Option	Description	runAssembly	runProject (Assembly)	gsAssembler
-rip	Flag to output each read in only one contig.	X	X	Reads limited to one contig toggle
-scaffold	Flag to enable output of the 454ScaffoldContigs.fna/qual file containing the scaffoldcontigs. An additional file, 454ContigScaffolds.txt, will be produced.	X	X	Output scaffolds toggle
-het	Flag to enable Heterozygotic mode	X	X	Heterozygotic mode toggle
-nohet	Flag to disable Heterozygotic mode	X	X	Heterozygotic mode toggle
-urt	Extend contigs using the ends (tips) of single reads	X	X	Use read tips
-it # (cDNA only)	Flag to specify the maximum number of isotigs in an isogroup. Default is 100 isotigs. Maximum is 10,000.	X	X	Parameters: Isotig Threshold
-ig # (cDNA only)	Flag to specify the maximum number of contigs in an isogroup. Default is 500 contigs.	X	X	Parameters: Isogroup Threshold
-icc # (cDNA only)	Flag to specify the maximum number of contigs in an isotig. Default is 100 contigs. Maximum is 200 and corresponds to the recursion depth during graph traversal.	X	X	Parameters: Isotig count threshold
-icl # (cDNA only)	Flag to specify the minimum length a contig must be to be part of an isotig. Default is 3 bp. Minimum is 0 bp. Some contigs slightly shorter than this may be included in isotigs due to the two-phase nature by which contig consensi are determined.	X	X	Parameters: Isotig length threshold
-isplit (cDNA only)	Initiate isotig traversal when depth spikes in alignments are found. These spikes will be treated as putative splice events so that traversal along the path will continue producing more isotigs.	X	X	n/a
-large	Flag to enable large genome assembly mode. This option should not be used in cDNA assembly projects.	X	X	Large or complex genome toggle
-nolarge	Flag to disable large genome assembly mode	X	X	Large or complex genome toggle

Table 5: Options Specific to Assembly