TagCleaner

Application data
Created by	Robert Schmieder
Biological application domain(s)	Transcriptomics, Metagenomics
Principal bioinformatics method(s)	Sequence trimming
Technology	Sanger, Illumina, 454, Ion Torrent, PacBio
Created at	San Diego State University, Sourceforge
Maintained?	Yes
Input format(s)	FASTA, FASTQ
Output format(s)	FASTA, FASTQ
Licence	GPLv3
Operating system(s)	UNIX, Mac OS X, Windows

Summary: TagCleaner can be used to automatically detect and efficiently remove tag sequences (e.g. WTA or MID tags) from metagenomic datasets. TagCleaner is available as both standalone and web-based versions.

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Description

Sequencing metagenomes that were pre-amplified with primer-based methods requires the removal of the additional tag sequences that can contain deletions or insertions due to sequencing limitations. The tag (e.g. WTA primer) sequence may be unavailable or incorrectly reported in public databases. Because of the potential for downstream inaccuracies introduced by unwanted sequence contaminations, it is important to use reliable tools for pre-processing sequence data.