CSC

Quality Clip

Description

This module determines where the sequence quality is too poor to use for reliable assembly. It supercedes the Uncalled Base Clip module. This uses the qclip program which reads and writes to Experiment Files. Its default quality evaluation is based on the range of values produced by the Estimate Base Accuracies module (quality value 70, averaged over 100 bases). For use with phred, try lower values such as quality value 15 averaged over 50 bases. When quality values are not available it will use the same method as the Uncalled Base Clip module; to analyse the base calls and count the number of undetermined bases within a given window of sequence. Both 5' and 3' ends may be quality clipped. For the confidence mode of clipping the method starts from the point of highest average quality, and then steps outwards in both directions until the average quality is below a defined threshold. For the sequence mode of clipping the method starts from a defined position and steps outwards in both directions until the number of uncalled bases within a given window length exceeds a predefined threshold. For more details see the qclip documentation (see section qclip). 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: Clip mode

This may be one of "by sequence" or "by confidence". The "by sequence" mode is equivalent to the Uncalled Clip module. The "by confidence" mode uses Phred-scaled confidence values to determine the quality for clipping. This does not work with eba confidence values.

Option: Minimum extent

The lowest allowable 5' clip position.

Option: Maximum extent

The largest allowable 3' clip position.

Option: Minimum length

If after quality clipping the good portion of a sequence is shorter than the specified length, then this file will be rejected with the message "qclip: Sequence too short".

Option: Window length

The window length over which the confidence will be averaged. This option is only relevant for the "clip by confidence" mode.

Option: Average confidence

The minimum average confidence (over `window length' bases) for sequence to be accepted as good quality. This option is only relevant for the "clip by confidence" mode.

Option: Start offset

The base number to start the 5' and 3' good quality searches from. This option is only relevant for the "clip by sequence" mode.

Option: 3' window length

The window length in which to count uncalled bases. This option is only relevant for the "clip by sequence" mode.

Option: 3' number of uncalled bases

The maximum allowed count of uncalled bases in a single window length. This option is only relevant for the "clip by sequence" mode.

Option: 5' window length

The window length in which to count uncalled bases. This option is only relevant for the "clip by sequence" mode.

Option: 5' number of uncalled bases

The maximum allowed count of uncalled bases in a single window length. This option is only relevant for the "clip by sequence" mode.