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

Background: 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. Results: 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 qualit...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Robert Schmieder, Yan Wei Lim, Forest Rohwer, Robert Edwards
• Keywords: Additional Tag Sequences, BMCBI 2010, Tag Sequences, Web Application