Screen Sequences

Description

This module can perform very fast matches between the sequences to process and one or more screen sequences. Any sequence containing a significant match is rejected. An example of use for this module is to reject sequences prior to assembly that appear to be contaminated with E. coli. This uses the screen_seq program (see section Screen_seq).

Option: Screen single sequence

This is yes/no question used to determine whether the screen sequence filename is the filename of a single sequence or a filename of a file containing a series of sequence filenames. To compare just one file select "Yes".

Option: Screen sequence file (of filenames)

This is either the filename of a single sequence or the filename of a file of filenames, depending on the answer to the previous question. The sequence files must be in plain text format containing just the bases or white space.

Option: Maximum screen sequence length

The maximum length of any individual screen sequence.

Option: Minimum match length

Any fragment containing an exact match longer than this length will be rejected.