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Table 5 Comparison of TagCleaner with other applications performing tag trimming

From: TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets

  TagCleaner PyroTagger RDP-Pyro SeqTrim SeqClean Mothur
Web-based Yes Yes Yes Yes - -
Standalone - Yes - Yes Yes Yes
Trim both ends Yes -1 Yes Yes Yes Yes
Provide trimming information2 Yes - Yes Yes Yes -
Support IUPAC
ambiguity codes
Yes Yes Yes - - Yes
# Allowed errors Any 0 0, 1, 2 Any3 Any3 0
Predict tag sequence Yes - - - - -
Detect fragment- to-fragment con- catenations Yes - - - - -
Continuous trimming4 Yes - - - - -
  1. The comparison is based on the features related to tag trimming, as this represents the main purpose of TagCleaner. All compared applications are still in active development and new functions will undoubtedly be added over time.
  2. 1 Performs barcode trimming at 5'-ends only.
  3. 2 Trimming position(s) and/or number of trimmed bases.
  4. 3 Percent similarity between tag sequence and query sequence (BLAST-based comparison).
  5. 4 Trimming of tag sequence repeats