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

Robert Schmieder12*, Yan Wei Lim3, Forest Rohwer3 and Robert Edwards14*

Author Affiliations

1 Department of Computer Science, San Diego State University, San Diego, CA, USA

2 Computational Science Research Center, San Diego State University, San Diego, CA, USA

3 Department of Biology, San Diego State University, San Diego, CA, USA

4 Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA

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BMC Bioinformatics 2010, 11:341  doi:10.1186/1471-2105-11-341

Published: 23 June 2010



Sequencing metagenomes that were pre-amplified with primer-based methods requires the removal of the additional tag sequences from the datasets. The sequenced reads can contain deletions or insertions due to sequencing limitations, and the primer sequence may contain ambiguous bases. Furthermore, the tag sequence may be unavailable or incorrectly reported. Because of the potential for downstream inaccuracies introduced by unwanted sequence contaminations, it is important to use reliable tools for pre-processing sequence data.


TagCleaner is a web application developed to automatically identify and remove known or unknown tag sequences allowing insertions and deletions in the dataset. TagCleaner is designed to filter the trimmed reads for duplicates, short reads, and reads with high rates of ambiguous sequences. An additional screening for and splitting of fragment-to-fragment concatenations that gave rise to artificial concatenated sequences can increase the quality of the dataset. Users may modify the different filter parameters according to their own preferences.


TagCleaner is a publicly available web application that is able to automatically detect and efficiently remove tag sequences from metagenomic datasets. It is easily configurable and provides a user-friendly interface. The interactive web interface facilitates export functionality for subsequent data processing, and is available at webcite.