N-Base Clipping

The purpose of this function is to remove runs of Ns or -s from the ends of sequences. Other bases may be interspersed in a run of dashes and the run will still be clipped, provided there are a sufficient number of non-A/C/G/T base calls. The exact algorithm for determining where a 'run' will stop is as follows:

1. Set score to zero
2. For each base call add 1 for N or -, -1 for A, C, G or T, zero for anything else.
3. Terminate when the score < -10.
4. Set the clip point at the highest score observed.

Generally this will have no effect (when on good data). It can never 'grow' a sequence (by extending the cutoffs into the good data). It will never form a hole in a contig by clipping all sequences in a region (as it will extend the data from both ends of the hole to join it back together again).