SeqTrim - A validation and trimming tool for all purpose sequence reads

Abstract

Bioinformatics tools are required to produce reliable, high quality data devoid of unwanted sequences in the preprocessing stage of current sequencing and EST projects. In this paper we describe SeqTrim, an algorithm designed to extract the insert sequence from any sequence read devoid of any foreign, contaminant or unwanted sequence, whatever the experimental process was. SeqTrim is easy to install and able to identify the sequence insert by removing low quality sequences, cloning vector, poly A or T tails, adaptors, and sequences that can be considered contaminants. It is easy to use and can be used as stand-alone application or as web page. The default parameters of the algorithm are best suited for most cases but a configuration file can be provided along with input sequences. SeqTrim admits several input and output formats (with and without quality values), which enables its inclusion in already or newly defined sequence processing workflows. SeqTrim is under continuous refinement due to collaboration between biologists and computer scientists which has succeed in correct dealing with most sequence cases and opens the possibility to include new capabilities to manage new kinds of bad sequences. © 2007 Springer-Verlag Berlin Heidelberg.