Based on the Qscore how much of my sequence should I keep? The error on next-gen sequencing increases linearly as you read the bases, therefore it can be dificult to draw a cut off-point. Here we fragment the sequence (user defined length) and check if the fragments mean Qscore are passing a Qscore threshold (user defined). The sequence is then build up one fragment at a time, once a fragment doesn't pass the Qscore threshold the remaining fragments are discarded.
Example:
Seq_1
'____________________________________'
fragment_1 - fragment_2 - fragment_3
'____________ ____________ ___________'
If fragments 1 & 3 pass the Qscore threshold and fragment_2 fails then the modified sequence will be:
Mod Seq_1
'____________'
fragment_1 - fragment_2 - fragment_3
Only fragment_1 is kept. A summary.txt file is outputed with the mean, median and std of modified sequence length and Qscore.