End Trimming parameters

End Trimming parameters determine how SeqMan Ultra trims data from the ends of sequences. SeqMan Ultra offers two ways to trim data, Quality or Fixed distance. Quality is the best choice if you are using data from an automated sequencer or if your sequence runs vary in length. Fixed distance is the recommended choice if your data are of a set length and do not have any quality or confidence measurements.

To access the dialog, use Project > Project Parameters. If the End Trimming section is not already active, click on End Trimming on the left. Note that end-trimming parameters are not applicable to BAM-based projects or .assembly projects.

To trim based on quality:

1. In the Select ends by menu, choose Quality

2. Use the Stringency menu to choose the stringency. Low, Medium, and High correspond to averaged quality score thresholds of 8, 12 and 16, respectively. These numbers appear in the Trace score threshold box just below the Stringency menu. If you choose Custom, you can enter your own value in the Trace score threshold box.

3. Enter the desired values into the two boxes in the Non-Trace Quality Settings section. SeqMan Ultra trims data from the ends based on the number of ambiguous residues (Ns) within each sliding window. In the Non-Trace Sequences section, you can choose the desired N window size and Maximum number of N’s. Example: If you set N window size to 70 and Maximum number of N’s to 2, SeqMan Ultra trims bases such that there are two or fewer Ns in the first and last 70 bases.

When you set up an assembly project in the Unassembled view, check the box next to Fixed Trim and click the Trim Now () tool to perform the trim prior to assembly.

To trim based on distance:

1. In the Select ends by menu, choose Fixed distance.

2. Enter the desired 5’ and 3’ trim points in the Fixed Trim Settings section. SeqMan Ultra will trim residues outside the boundaries you specify.

When you set up an assembly project in the Unassembled view, check the box next to Quality Trim and click the Trim Now () tool to perform the trim prior to assembly.

*Note: You can edit End Trimming parameters to switch between the two trim types even if you are midway through setting up a project in the Unassembled view.