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Genomics. 2013 Nov-Dec;102(5-6):500-6. doi: 10.1016/j.ygeno.2013.07.011. Epub 2013 Aug 1.

AlienTrimmer: a tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads.

Author information

1
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.
2
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.

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/.

KEYWORDS:

Adapter oligonucleotides; High-throughput sequencing; Polynomial algorithm; Raw read trimming; Short contaminant sequence; k-mer decomposition

PMID:
23912058
DOI:
10.1016/j.ygeno.2013.07.011
[Indexed for MEDLINE]
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