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
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
- 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
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Last generated on 2 Febuary 1999.