GS De Novo Assembler cDNA / Transcriptome Options

1.14	GS De Novo Assembler cDNA / Transcriptome Options

These descriptions are for options specific to cDNA / transcriptome assembly projects:

Option	Description
-cdna	cDNA / Transcriptome assembly - To specify a cDNA / transcriptome assembly project, use the -cdna option with the runAssembly or newAssembly commands.
-ig	Isogroup Threshold - Specifies the maximum number of contigs in an isogroup. If an isogroup has more contigs than this threshold, it will not be traversed for isotigs and its contigs will appear as contigs in the output files.
-it	Isotig Threshold - Specifies the maximum number of isotigs in an isogroup. When this threshold is reached, the isogroup traversal will stop and all of its contigs will appear as contigs in the output files.
-icc	Isotig Contig Count Threshold - Specifies the maximum number of contigs in one isotig. When this threshold is reached, the further traversal of a particular isotig in an isogroup will be stopped and the isotig's contigs might or might not appear as contigs in the output files, depending on whether that particular contig is part of another isotig in an isogroup; only the contigs which are not part of any isotig will be reported as contigs in the output files.
-icl	Isotig Contig Length Threshold - If any contig length is shorter than this threshold, the further traversal of a particular isotig in an isogroup will be stopped. The contig shorter than the icl threshold will be marked as such and reported in the output files. Other contigs from such an isotig might or might not appear as contigs in the output files, depending on whether each particular contig is part of another isotig in an isogroup; only the contigs which are not part of any isotig will be reported as contigs in the output files. Rarely, a contig with a reported length below this threshold will be traversed in an isotig. This is because the contig length estimated prior to final basecalling is the length tested against the –icl threshold. The reported length of the contig may change slightly when basecalling occurs. It is also possible for isotig traversal to stop at a contig whose reported length is above the –icl threshold.
-isplit	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.

For cDNA assembly, the “-a” is set to 0 regardless of the value that may be entered on the command-line.

If any of the above-mentioned thresholds are set to zero, it will not be taken into account during the computation. In such cases, some implicit thresholds and limits may still be applied as described below. Default thresholds for the computation are:

•	ig = 500 contigs

•	it = 100 isotigs

•	icc = 100 contigs

•	icl = 3 base pairs

Implicit thresholds and limits for the computation (imposed due to the recursive nature of traversal algorithm) are:

•	Maximum recursion depth during isotig path traversal is 200. This corresponds to the number of contigs in the isotig, i.e. the -icc threshold.

•	Maximum isotig count during graph traversal is 10000. This corresponds to the number of isotigs in the isogroup, i.e. the -it threshold.

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Cyclic graphs: recursive isotig path traversal will stop if cyclic isotig structures are detected, i.e. revisiting one contig which has already been part of the isotig being traversed. Such cyclic structures will be marked in the output files by assigning cyclic status for the first contig detected, and the cyclic isotig's contigs might or might not appear as contigs in the output files, depending on whether each particular contig is part of another non-cyclic isotig in an isogroup.

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Edge Threshold: is used when an edge's depth is less than 5% of the maximum of the "end" column depths of the two chords that the edge connects. "End" column means the alignment column of the end of the chord connected to the edge. Whenever an edge depth is less that this 5% threshold, isotig traversal ends and the chord that the edge leads to is left as a contig. These contigs are never removed from the isogroup.

The Large or complex genome option should not be used in cDNA assembly projects, and use of the -e and –het options is not recommended.