Tag Repeats

Description

This module uses the repe program to identify and mark known repetitive elements within the sequences. An example usage is to tag all ALU fragments. This information may be used by the gap4 assembly algorithm to improve the assembly by initially ignoring matches between two ALU fragments which may otherwise produce incorrect assemblies. If available, we recommend using RepeatMasker instead of this module.

Option: Repeat file name

This is the filename of a file of filenames, each of which contain a single repeat to search for. The format of these individual files is plain text consisting of just the nucleotides and white space.

Option: Repeat score

This is the minimum score for classifying a matched segment as a repeat.

Option: Tag type

This is the gap4 tag type to use for identifying this repeat segment. It is not possible to choose different tag types for different repeats, although the tag comments contain the match score and match filename.