Trace Quality Clip

Filename

trace_clip.p4m

Description

This module determines where the sequence quality is too poor to use for reliable assembly. This uses the trace_clip program which reads and writes to Experiment Files. Its quality evaluation is based on analysis of the chromatogram files. Both 5' and 3' ends may be quality clipped. For more details see the trace_clip and scale_trace_clip documentation (see section Trace Clipping). Note that the Phrap assembly algorithm works best without quality clipping and it can make use of the full length of readings (due to the use of the Phred confidence values).

Option: Ends to clip

This controls whether 5', 3' or both ends should be quality clipped.

Option: Maximum right clip

The largest allowable 3' clip point.

Option: Minimum left clip

The lowest allowable 5' clip point.

Option: Start point

The base number from which to search (in both directions) along the good data. If this is set to -1 the program will pick a sensible start point.

Option: Trace_clip arguments

This defines any additional command line arguments to send to the trace_clip program.