title: AlienTrimmer: a tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads.
abstract: Contaminant oligonucleotide sequences such as primers and adapters can occur in both ends of high-throughput sequencing (HTS) reads. AlienTrimmer was developed in order to detect and remove such contaminants. Based on the decomposition of specified alien nucleotide sequences into k-mers, AlienTrimmer is able to determine whether such alien k-mers are occurring in one or in both read ends by using a simple polynomial algorithm. Therefore, AlienTrimmer can process typical HTS single- or paired-end files with millions of reads in several minutes with very low computer resources. Based on the analysis of both simulated and real-case Illumina®, 454™ and Ion Torrent™ read data, we show that AlienTrimmer performs with excellent accuracy and speed in comparison with other trimming tools. The program is freely available at ftp://ftp.pasteur.fr/pub/gensoft/projects/AlienTrimmer/.
authors.affiliation: Institut Pasteur, Genotyping of Pathogens and Public Health Platform (PF8), 28 rue du Dr Roux, 75724 Paris Cedex, France; Institut Pasteur, Microbial Evolutionary Genomics Unit, 28 rue du Dr Roux, 75724 Paris Cedex, France; CNRS, UMR3525, 75015 Paris, France. Electronic address: alexis.criscuolo@pasteur.fr.
authors.forename: Alexis
authors.initials: A
authors.lastname: Criscuolo
authors.affiliation: Institut Pasteur, Genotyping of Pathogens and Public Health Platform (PF8), 28 rue du Dr Roux, 75724 Paris Cedex, France; Institut Pasteur, Microbial Evolutionary Genomics Unit, 28 rue du Dr Roux, 75724 Paris Cedex, France; CNRS, UMR3525, 75015 Paris, France.
authors.forename: Sylvain
authors.initials: S
authors.lastname: Brisse
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology; D004247:DNA / Q000235:genetics*; D059018:DNA Contamination; D017931:DNA Primers; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D011786:Quality Control; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D017931:DNA Primers; D004247:DNA
keywords: Adapter oligonucleotides; High-throughput sequencing; Polynomial algorithm; Raw read trimming; Short contaminant sequence; k-mer decomposition