Trim by Sequences
NextGENe allows for trimming by sequences in two cases:
• The sequence has an error in it.
• Only part of the sequence is present.
In these situations, NextGENe breaks the input sequence into smaller segments and checks the read for the small segments instead of the whole sequence.
• If the input sequence is >= 16 bp, then it is broken into small segments with a length of 12 bp.
• If the input sequence is < 16 bp but > 7 bp, then it is broken into small segments with a length of 8 bp.
• If the input sequence is < 8 bp but > 3 bp, then it is broken into small segments with a length of 4 bp.
 | No mismatches are allowed for an input sequence < 4 bp. |