This screen appears in long read workflows and pertains to the short read sequences being used to refine a long-read assembly. Some workflows call this the Polishing Options screen, while others call it the Short Read Polishing Options screen, but both screens are identical.
|Category||Options and Descriptions|
|Pre-assembly Options||Check Maximum total reads and enter a value if you wish to limit the read depth. Utilizing this option can make the assembly proceed faster.|
|Assembly Options|| Mer size is the minimum length of a mer (overlapping region of a fragment read), in bases, required to be considered a match when arranging reads into contigs. Mer size information is used to identify matches during the assembly layout phase. The default mer size is determined by the selected read technology and is shown in the window. For more information, see How mer tags are chosen.
| Minimum match % specifies the minimum percentage of matches in an overlap required to join two sequences in the same contig. SeqMan NGen determines the percentage to use based on the sequencing technology you specified in the Assembly Options dialog. For more information, see Calculation of match percentage.
|Post-assembly Options|| The Minimum contig size requirements options direct SeqMan NGen to remove assembled, untemplated contigs that do not meet minimum thresholds. This can lead to a desirable decrease in project size. Choose whether to use the Default values or enter Custom values. If you choose the latter, enter values for the following:
Click Next > to proceed to the next wizard screen or < Back to return to the previous screen.
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