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(Short Read) Polishing Options

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.

  • Automatic – Select this button to automatically set the size based on assembly type and sequencing technology.

  • Custom – Select this button to choose the size yourself. You must enter the desired number of base pairs in the field at right. Lowering the mer size increases the sensitivity of finding matches, but also increases the likelihood of finding spurious matches in addition to the correct match. Lowering the mer size can also greatly increase the requirements for storing intermediate and temporary files with large projects.
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.

  • Automatic – Select this button to automatically set the percentage based on assembly type and sequencing technology.

  • Custom – Select this button to designate the percentage yourself. You must enter a number in the field at right.
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:


  • Min sequences – Disassembles any untemplated contigs with fewer than the specified number of sequences. This option affects only untemplated contigs. No templated contigs are removed.

  • Min length – Using this option disassembles any untemplated contigs shorter than the specified length.This option affects only untemplated contigs. No templated contigs are removed.

Click Next > to proceed to the next wizard screen or < Back to return to the previous screen.

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