SeqTrim07: a pipeline for preprocessing sequence reads Online publication date: Sun, 23-Jan-2011
by Juan Falgueras, Antonio J. Lara, Guillermo Perez-Trabado, Noe Fernandez-Pozo, Francisco R. Canton, M. Gonzalo Claros
International Journal of Computational Intelligence in Bioinformatics and Systems Biology (IJCIBSB), Vol. 1, No. 4, 2010
Abstract: SeqTrim is a pipeline designed to preprocessing sequence reads. It is easy to install and configure, flexible even if default parameters are accurate for most purposes and usable as a web interface or a standalone command line application. It identifies the sequence insert by removing low quality sequences, cloning vector, poly-A or poly-T tails, adaptors and any contaminant sequence or unwanted feature. Several input and output formats are available, which enables its inclusion in already or newly defined sequence processing work flows. It outperforms preprocessors implemented in other web servers and standalone applications at least in detecting adaptors and chimeric clones. SeqTrim is under continuous refinement to deal with most sequence events due to collaboration between biologists and computer scientists.
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