Related Experiment Video
Updated: May 9, 2026
Introductory Analysis and Validation of CUT&RUN Sequencing Data
Published on: December 13, 2024
AlienTrimmer: a tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput
Alexis Criscuolo1, Sylvain Brisse1
1Institut 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.
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/.
