Table 5

Comparison of TagCleaner with other applications performing tag trimming

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

-

-

-

-

-


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.

1 Performs barcode trimming at 5'-ends only.

2 Trimming position(s) and/or number of trimmed bases.

3 Percent similarity between tag sequence and query sequence (BLAST-based comparison).

4 Trimming of tag sequence repeats

Schmieder et al. BMC Bioinformatics 2010 11:341   doi:10.1186/1471-2105-11-341

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