SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read

Background: High-throughput automated sequencing has enabled an exponential growth rate of sequencing data. This requires increasing sequence quality and reliability in order to avoid database contamination with artefactual sequences. The arrival of pyrosequencing enhances this problem and necessitates customisable preprocessing algorithms. Results: SeqTrim has been implemented both as a Web and as a standalone command line application. Alreadypublished and newly-designed algorithms have been included to identify sequence inserts, to remove low quality, vector, adaptor, low complexity and contaminant sequences, and to detect chimeric reads. The availability of several input and output formats allows its inclusion in sequence processing workflows. Due to its specific algorithms, SeqTrim outperforms other pre-processors implemented as Web services or standalone applications. It performs equally well with sequences from EST libraries, SSH libraries, genomic DNA libraries and pyrosequenci...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Juan Falgueras, Antonio J. Lara, Noé Fernández-Pozo, Francisco R. Cantón, Guillermo Pérez-Trabado, M. Gonzalo Claros
• Keywords: BMCBI 2010, Customisable Preprocessing Algorithms, Exponential Growth Rate, Sequences