Project Computation Sub-Tab

1.7.2

The Computation sub-tab is shown on Figure 13. It allows you to adjust the settings described below.

Figure 13: gsAssembler Parameters tab, Computation sub-tab for Genomic projects

•

Incremental De Novo assembler analysis – Results from computations performed with this option selected (checked) will serve as the basis for the assembly of additional reads. If a project computation is performed with this option deselected, all the project data will be assembled anew each time it is computed, i.e. forcing all alignments to be recalculated and overwriting any existing assembly results.

◦	Default: selected (Note: This setting is not saved with a project, and is always reset to “selected” when a project is re-opened).

•

The number of CPUs option can be given to limit the load of the software on the computing resources. The default is 1, which specifies that one of the CPUs on the computer should be used. The computation uses the CPU setting to create an approximate load on the computer, so the actual load may vary somewhat from this number, i.e., using “-cpu 3” may cause a load from 2 to 4 on the system.

Currently, only the “Computing alignments…”, “Mapping short reads to consensi…”, and “Generating output…” phases have been parallelized (because they are the most computationally intensive phases for larger projects). Other phases of the computation will still use single threading. The parallel assembler only runs on shared memory, i.e. only CPUs with access to the same physical memory can be used.

The current memory footprint is 3 bytes per input (read) base. For example a 1 Gbp genome with a 20x coverage would need 60 GB of physical memory. Please note that the memory footprint can increase when working with a genome containing high-copy count repeat sequences, or when using multiple cpus.

•

Use duplicate reads – when checked, the Assembler will include duplicate reads when computing the consensus for a contig. Duplicate reads are a known potential artifact of the emPCR Amplification process which may occur, for example, when two or more beads are amplified in a single emulsion microreactor. In such cases, duplicate reads should be excluded from the computations, which is the default.

•

Use serial I/O – select this option if you are using many .sff files (> 4 million reads) in your project. The option instructs the software to prepare an intermediate read file in which the reads appear in the same order as they do in the alignments. For large projects, this can speed up the execution of the Assembler, especially during the Output Phase of its computation. For more information, see Section 4.6.

•

Extend low depth overlaps – select this option to instruct the assembler to extend contigs even when the depth falls to a single read. This option can be especially useful as a means to obtain more complete contigging across low-depth portions of genomic and transcriptomic assemblies. For more information, see Section 4.12 on the –urt option.

•	Overlap Detection Parameters:

Parameter	Description	Default Value	Allowed Values
Seed step	The number of bases between seed generation locations used in the exact k-mer matching part of the overlap detection.	12	>= 1
Seed length	The number of bases used for each seed in the exact k-mer matching part of the overlap detection (i.e. the “k” value of the k-mer matching).	16	6 - 16
Seed count	The number of seeds required in a window before an extension is made.	1	>= 1
Minimum overlap length	The minimum length of overlaps used by the assembler for the pairwise alignment step. This value can be entered as either a number of bases or a percent of read length. To enter a percent, the % symbol must be used (e.g. 37%).	40	>= 1 (length) 1 – 100 (percent)
Minimum overlap identity	The minimum percent identity of overlaps used by the assembler for the pairwise alignment step.	90	0 - 100
Alignment identity score	When multiple overlaps are found, the per-overlap-column identity score used to sort the overlaps for use in the progressive alignment.	2	>= 0
Alignment difference score	When multiple overlaps are found, the per-overlap-column difference score used to sort the overlaps for use in the progressive multi-alignment.	-3	<= 0

For a description of the overlap detection parameters for assembly, please see Table 4 in the Appendix section.