This tool uses cross_match to mask vector/adapter sequences and optinaly trim vector sequence and/or polyA/T trail.
It takes a set of sequences to be masked, and a set of vectors/adapters used to perform masking.
Cross_match relies on alignment algorithms and needs two parameters:
- minmatch: length of word witch exact match used to anchor alignment
- minscore: minimal score to reach for an alignment to be reported.
If vector sequences are unknown, or if you want to check for other contaminations, you can add optionaly sequences from Univec or UnivecCore (?).
Cross_match Result Files