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Fraction of reads to use
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The default setting of 100% is recommended, and handles most changes in coverage. If you enter a value of less than 100%, the reads are randomly sub-sampled.
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Only process barcodes
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By default, the plugin processes all barcodes in the analysis and produces a separate set of contigs for each barcode. To limit plugin analysis to only specific barcodes, list those barcodes here (separated by commas and no spaces. For example, IonXpress_001,IonXpress_002,IonXpress_003).
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Skip barcodes with fewer than __ reads
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The software ignores barcodes whose number of reads do not meet the threshold specified here. The default threshold is 500 reads. This setting is intended to filter out barcode classification problems with noisy data.
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RAM to allocate
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The plugin attempts to allocate the specified amount of RAM when it runs. The default is 32 GB. With larger amounts of memory, the plugin runs faster. With less memory, the plugin takes longer to complete.
Note:
The plugin crashes if the memory allocation fails.
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SPAdes version
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Select the version that you prefer. Select the default of
3.1.0 if you are not sure.
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Assembly settings
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Set this menu as follows:
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Uniform coverage (default setting)—This is used for data with average GC (35–68%) content. This setting uses the default kmers.
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Non-uniform coverage—Choose this setting for data with low GC (<35%) content. This setting uses the default kmers.
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Highly non-uniform coverage—Choose this setting for data with high GC (>68%) content. This setting uses a different set of kmers.
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Custom…—Choose this setting to enter user-defined
K and
Mode settings.
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K—Enter values (separated by commas, no spaces) to determine the size and number of kmers to be used in the analysis. Enter short kmer values to improve error-prone or low-coverage regions, long kmers to resolve repetitive regions, or a combination of kmer values to account for both situations.
Note:
Each additional kmer adds a fixed amount to the processing time (for example, using 2 kmers takes twice as long as 1 kmer).
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Mode—Select
Multi-cell (default) for data with average or low GC content. Select
Single-cell for data with high GC (>68%) content.
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Run read correction before doing assembly
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This setting is enabled by default, which is recommended.
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Skip assembly if previous results exist
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Select this checkbox to detect whether assembly results already exist and you do not want to overwrite the results.
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